2023-01-05T00:18:12,474 Created temporary directory: /tmp/pip-ephem-wheel-cache-ebknz63b 2023-01-05T00:18:12,476 Created temporary directory: /tmp/pip-build-tracker-nk6mpxmq 2023-01-05T00:18:12,476 Initialized build tracking at /tmp/pip-build-tracker-nk6mpxmq 2023-01-05T00:18:12,476 Created build tracker: /tmp/pip-build-tracker-nk6mpxmq 2023-01-05T00:18:12,477 Entered build tracker: /tmp/pip-build-tracker-nk6mpxmq 2023-01-05T00:18:12,477 Created temporary directory: /tmp/pip-wheel-38g4xyr9 2023-01-05T00:18:12,480 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. 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https://files.pythonhosted.org/packages/8a/3d/34bc8f592d832ec464e427ecf09c62898a128a41c3f1ae142a1d9f9f2646/MDAnalysis-2.4.1-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,622 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/a4/3f/c3961c791f4ab6128fbde66d5829b53d8e89a67ac3d4c23850b58c267206/MDAnalysis-2.4.1-cp38-cp38-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,623 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/3d/59/1a669cb57701c883c0b2e36742fd5d7a250a71fc24e369c57db71496481f/MDAnalysis-2.4.1-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,623 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/64/3f/4a0d22c2b5bad72be6c07c31c6e9e870e6b3a50142edc97962830bbe22ad/MDAnalysis-2.4.1-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,623 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/83/d8/e99fcc0339181b0ffe3fac620f884241bd502bb392696e2429984c3ea81d/MDAnalysis-2.4.1-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,624 Found link https://files.pythonhosted.org/packages/8f/c0/eba86324ca52fe66db629a4d805729ad8ac3364e3adad532c063b52b7051/MDAnalysis-2.4.1.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.4.1 2023-01-05T00:18:12,624 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/39/ae/52d836a64c4094794580daf0d2692fa95d244be6321fa17e6d45fe35f621/MDAnalysis-2.4.2-cp310-cp310-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,624 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/69/c7/3dfe97658982390bbf93cf97f4aabb22025d2956bcd82b410e8c1831dfac/MDAnalysis-2.4.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,624 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/73/74/abcb7c91e47f350db0268c2058f079c937bb2f337d73b62ca3b8dea4642e/MDAnalysis-2.4.2-cp310-cp310-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,625 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/f1/34/7eedce6129f71fa38fbf9d7fe3a8f366ddee3142afb07113598bf2b66d81/MDAnalysis-2.4.2-cp311-cp311-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,625 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/ee/40/20322a888419cc4aeaafa552c51c97c666a46e69c0d130dc5744ec04ae58/MDAnalysis-2.4.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,625 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/8b/65/c72765a2a6c73b8e03e114cf7e1661c28df3049adc42e8c75838b48ca083/MDAnalysis-2.4.2-cp311-cp311-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,625 Skipping link: No binaries permitted for mdanalysis: 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https://files.pythonhosted.org/packages/89/9a/8e6cdd8c6da04926bbaea76877b9b17082b77db742a82074b2c6dfb85e99/MDAnalysis-2.4.2-cp39-cp39-macosx_10_9_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,626 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/19/cc/840974bc7109839cdef50cc049336cefb2a4acc44f68913eec5f0d4db458/MDAnalysis-2.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,626 Skipping link: No binaries permitted for mdanalysis: https://files.pythonhosted.org/packages/89/37/ee29c83d622e3d55a2e2936d70cf3f3d74beaf28d5d5747385e2f9149ec8/MDAnalysis-2.4.2-cp39-cp39-win_amd64.whl (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,627 Found link https://files.pythonhosted.org/packages/7d/6b/f0ea2ab44ed0a2448737d779e02d3ae719c186dc9e3ce4cd0d75b4026dcc/MDAnalysis-2.4.2.tar.gz (from https://pypi.org/simple/mdanalysis/) (requires-python:>=3.8), version: 2.4.2 2023-01-05T00:18:12,627 Fetching project page and analyzing links: https://www.piwheels.org/simple/mdanalysis/ 2023-01-05T00:18:12,627 Getting page https://www.piwheels.org/simple/mdanalysis/ 2023-01-05T00:18:12,628 Found index url https://www.piwheels.org/simple 2023-01-05T00:18:12,795 Fetched page https://www.piwheels.org/simple/mdanalysis/ as text/html 2023-01-05T00:18:12,825 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.4.1-cp39-cp39-linux_armv7l.whl#sha256=f6908b1d7ccb4f424abc3a05af2e41727e6d4b0a4fdb40f03dd0286a667f100f (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.8) 2023-01-05T00:18:12,825 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp37-cp37m-linux_armv7l.whl#sha256=15211cf0c7bf4819d9c48762d3c10d7541b273818dfe16cade585528469acb6e (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2023-01-05T00:18:12,828 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.1.0-cp37-cp37m-linux_armv6l.whl#sha256=15211cf0c7bf4819d9c48762d3c10d7541b273818dfe16cade585528469acb6e (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.7) 2023-01-05T00:18:12,828 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0-cp39-cp39-linux_armv7l.whl#sha256=565f74ce6e9dd72729736ca534c18c243dfa384a984c24dd759f1a263cd3c98c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=3.6) 2023-01-05T00:18:12,828 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-2.0.0b0-cp37-cp37m-linux_armv6l.whl#sha256=331239f905d05b614d662e8a60615f80c2611d8f6ea8f3e256a0cbcefdf53191 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,829 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.1-cp37-cp37m-linux_armv7l.whl#sha256=636760cd892a8524f5912fafc58d29ffcce61acbd8730c7c69a3e922a164476f (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2023-01-05T00:18:12,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.1-cp37-cp37m-linux_armv6l.whl#sha256=636760cd892a8524f5912fafc58d29ffcce61acbd8730c7c69a3e922a164476f (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2023-01-05T00:18:12,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.0-cp37-cp37m-linux_armv7l.whl#sha256=9693d11a44eeb74415f6614dca0791bfe7f0cf24552a0ed3d17c133ff5b361ef (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2023-01-05T00:18:12,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.1.0-cp37-cp37m-linux_armv6l.whl#sha256=9693d11a44eeb74415f6614dca0791bfe7f0cf24552a0ed3d17c133ff5b361ef (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,<3.9) 2023-01-05T00:18:12,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv7l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2023-01-05T00:18:12,830 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.1-cp37-cp37m-linux_armv6l.whl#sha256=1214ca3490e50243b48350c6c6a2c89b77cce8f1cd72f6d2549860b3db1ad84c (from https://www.piwheels.org/simple/mdanalysis/) (requires-python:>=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3,!=3.4.*,<3.9) 2023-01-05T00:18:12,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp39-cp39-linux_armv7l.whl#sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp39-cp39-linux_armv6l.whl#sha256=e43dbbd4ecd06fb475d80e5dae571708415e1287e6dd2c669c98095e13ea2ae8 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp37-cp37m-linux_armv7l.whl#sha256=1368159b6134befa021a6536dcc02e047dc27b4c4672ae7f3b2f8e1559b43f8e (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp37-cp37m-linux_armv6l.whl#sha256=1368159b6134befa021a6536dcc02e047dc27b4c4672ae7f3b2f8e1559b43f8e (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,831 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-1.0.0-cp35-cp35m-linux_armv6l.whl#sha256=b669220c967a8cc746ae35c931d22da666f540595d1e9a9c3bb620effa9205b3 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,832 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp39-cp39-linux_armv7l.whl#sha256=71f4f4953090bbbbafab4e8e5f1af9286acd1dbe6863f95771e62ca51d6772be (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,834 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp39-cp39-linux_armv6l.whl#sha256=71f4f4953090bbbbafab4e8e5f1af9286acd1dbe6863f95771e62ca51d6772be (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,834 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.20.0-cp37-cp37m-linux_armv7l.whl#sha256=9b6fa10f5b5f2473db79f5704fbfc697f53d7c356f152ba8d80c761e63acbed7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,834 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv7l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,839 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp35-cp35m-linux_armv6l.whl#sha256=66b3e7f35c28b424a6ad19307554c223ebc24916dddb557dbd08762989c32119 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,839 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.18.0-cp37-cp37m-linux_armv6l.whl#sha256=07e291f5c3ee08d16b280c629411107ae1984f33458036e3418429e5f1a33092 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,839 Skipping link: No binaries permitted for mdanalysis: 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https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv6l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,840 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp34-cp34m-linux_armv7l.whl#sha256=ca0488c00e0be959cac05340ae1deb148c2769996e5abb346ad3a7487c2193d1 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,840 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv6l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,840 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.17.0-cp35-cp35m-linux_armv7l.whl#sha256=58492c63068e648dfb1879b19f1fa55e6e3b9589ee9141eda53c4aed5a915136 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,840 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv6l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,841 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp35-cp35m-linux_armv7l.whl#sha256=28e395835220893e8a10d101072b742e6401a4376ddfacc41e30572d8aa6ed65 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,841 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv6l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,841 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.2-cp34-cp34m-linux_armv7l.whl#sha256=e959b452e988fe4a9b8459143d6a64eef168bc3b9355a04b20ba20c4bb1bf601 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,841 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv6l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,841 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp34-cp34m-linux_armv7l.whl#sha256=985988f3d88079fe20f14ddee546fbb7b13e2a70dbeb4ac10c0f38f45afa7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,842 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv7l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,842 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.1-cp35-cp35m-linux_armv6l.whl#sha256=933bf37f65e3ae59c832a6798365a3da99432510fcfc802e2d6eaa48db3a7261 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,842 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv6l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,842 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp34-cp34m-linux_armv7l.whl#sha256=34198e0f9e509df1779c2255812cee0f720dc8e989c7d4b7196337f75f1ef51b (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,842 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv7l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,843 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.16.0-cp35-cp35m-linux_armv6l.whl#sha256=032867bf17eecd5fd249607198ad5c191fac901f2856d5a485ffc53a8eb687d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,843 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv7l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,843 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp35-cp35m-linux_armv6l.whl#sha256=04685acd7ab3d9f580c6dccdc18dfa33d89ea596521eede98bef2ec3f8f58af7 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,843 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv6l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,844 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.15.0-cp34-cp34m-linux_armv7l.whl#sha256=30c2bb9cf26e969dbdc8978bd4710e9e8a42ee42ed7c9ad506c63a0855448307 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,844 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv6l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,844 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp34-cp34m-linux_armv7l.whl#sha256=527918d821e76043cda119ee29aa26b835f8f85251d560d47616e9147b5a1539 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,844 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv6l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,844 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.14.0-cp35-cp35m-linux_armv7l.whl#sha256=b9d6e5734efb33b9383183904d491de8ef28aeeac7bbfdd617d48084126af113 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,845 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv7l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,845 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp39-cp39-linux_armv6l.whl#sha256=ef25ee9269f3b7f8ab95f1c3c563c39740fd2b7801df49d6be7e702c7db7f8fc (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,845 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv7l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,845 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp35-cp35m-linux_armv6l.whl#sha256=46ca86446af4c56b5805a1cb36dd77ac64d009abb5500878ea4fa26320c7ba43 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,845 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv6l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,846 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp34-cp34m-linux_armv7l.whl#sha256=89151b95fc0cd948f7a2d1d660b8c2453a612a752a2a2d7d8fb6d169ff2782d4 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,846 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv7l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,846 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.13.0-cp37-cp37m-linux_armv6l.whl#sha256=a073eda71f157be82bd9b81ac12793e63834dde1ac9b63ca704668a88b025c1e (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,846 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv7l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,846 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp35-cp35m-linux_armv6l.whl#sha256=47de147e5ee68a99b75107632aaa1e3bf84b4fa1f5bd7a456c1537266d437fbb (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,847 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv6l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,847 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.12.1-cp34-cp34m-linux_armv7l.whl#sha256=a0ddeb70a574aee9a5c491f2da635dc26e5e5b2b4cac7d8abbbffb3c1b4c7a8a (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,847 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv6l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,847 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp35-cp35m-linux_armv7l.whl#sha256=28a9bbed8fd84f6ebdf4efb48ef9e2435715169ef7a558ad7f11a33232e83815 (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,847 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv6l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,848 Skipping link: No binaries permitted for mdanalysis: https://www.piwheels.org/simple/mdanalysis/MDAnalysis-0.11.0-cp34-cp34m-linux_armv7l.whl#sha256=6d813f8dee5bde52fe344b851079bfaab34030f253869d7098ee33929566e36a (from https://www.piwheels.org/simple/mdanalysis/) 2023-01-05T00:18:12,848 Skipping link: not a file: https://www.piwheels.org/simple/mdanalysis/ 2023-01-05T00:18:12,848 Skipping link: not a file: https://pypi.org/simple/mdanalysis/ 2023-01-05T00:18:12,871 Given no hashes to check 1 links for project 'mdanalysis': discarding no candidates 2023-01-05T00:18:12,888 Collecting mdanalysis==2.4.2 2023-01-05T00:18:12,890 Created temporary directory: /tmp/pip-unpack-c21zq6as 2023-01-05T00:18:13,407 Downloading MDAnalysis-2.4.2.tar.gz (3.7 MB) 2023-01-05T00:18:16,445 Added mdanalysis==2.4.2 from https://files.pythonhosted.org/packages/7d/6b/f0ea2ab44ed0a2448737d779e02d3ae719c186dc9e3ce4cd0d75b4026dcc/MDAnalysis-2.4.2.tar.gz to build tracker '/tmp/pip-build-tracker-nk6mpxmq' 2023-01-05T00:18:16,498 Created temporary directory: /tmp/pip-build-env-4g47ji3o 2023-01-05T00:18:16,505 Installing build dependencies: started 2023-01-05T00:18:16,506 Running command pip subprocess to install build dependencies 2023-01-05T00:18:17,693 Using pip 22.3 from /usr/local/lib/python3.9/dist-packages/pip (python 3.9) 2023-01-05T00:18:18,106 DEPRECATION: --no-binary currently disables reading from the cache of locally built wheels. In the future --no-binary will not influence the wheel cache. pip 23.1 will enforce this behaviour change. A possible replacement is to use the --no-cache-dir option. You can use the flag --use-feature=no-binary-enable-wheel-cache to test the upcoming behaviour. Discussion can be found at https://github.com/pypa/pip/issues/11453 2023-01-05T00:18:18,131 Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple 2023-01-05T00:18:18,133 Ignoring numpy: markers 'python_version == "3.8" and (platform_machine != "arm64" or platform_system != "Darwin") and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,134 Ignoring numpy: markers 'python_version == "3.8" and platform_machine == "arm64" and platform_system == "Darwin" and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,136 Ignoring numpy: markers 'python_version == "3.9" and platform_machine == "arm64" and platform_system == "Darwin" and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,137 Ignoring numpy: markers 'python_version == "3.10" and platform_system == "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,138 Ignoring numpy: markers 'python_version == "3.10" and platform_system != "Windows" and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,139 Ignoring numpy: markers 'python_version == "3.11" and platform_python_implementation != "PyPy"' don't match your environment 2023-01-05T00:18:18,140 Ignoring numpy: markers 'python_version >= "3.12"' don't match your environment 2023-01-05T00:18:19,692 Collecting Cython>=0.28 2023-01-05T00:18:20,208 Using cached https://www.piwheels.org/simple/cython/Cython-0.29.32-cp39-cp39-linux_armv7l.whl (5.0 MB) 2023-01-05T00:18:20,642 Collecting packaging 2023-01-05T00:18:20,688 Using cached https://www.piwheels.org/simple/packaging/packaging-22.0-py3-none-any.whl (42 kB) 2023-01-05T00:18:22,286 Collecting numpy==1.20.0 2023-01-05T00:18:25,853 Using cached https://www.piwheels.org/simple/numpy/numpy-1.20.0-cp39-cp39-linux_armv7l.whl (11.6 MB) 2023-01-05T00:18:27,677 Collecting setuptools 2023-01-05T00:18:27,826 Using cached https://www.piwheels.org/simple/setuptools/setuptools-65.6.3-py3-none-any.whl (1.2 MB) 2023-01-05T00:18:28,113 Collecting wheel 2023-01-05T00:18:28,133 Using cached https://www.piwheels.org/simple/wheel/wheel-0.38.4-py3-none-any.whl (36 kB) 2023-01-05T00:18:30,144 Installing collected packages: wheel, setuptools, packaging, numpy, Cython 2023-01-05T00:18:30,288 Creating /tmp/pip-build-env-4g47ji3o/overlay/bin 2023-01-05T00:18:30,290 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/wheel to 755 2023-01-05T00:18:40,895 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/f2py to 755 2023-01-05T00:18:40,897 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/f2py3 to 755 2023-01-05T00:18:40,900 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/f2py3.9 to 755 2023-01-05T00:18:43,713 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/cygdb to 755 2023-01-05T00:18:43,716 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/cython to 755 2023-01-05T00:18:43,718 changing mode of /tmp/pip-build-env-4g47ji3o/overlay/bin/cythonize to 755 2023-01-05T00:18:43,745 Successfully installed Cython-0.29.32 numpy-1.20.0 packaging-22.0 setuptools-65.6.3 wheel-0.38.4 2023-01-05T00:18:43,760 [notice] A new release of pip available: 22.3 -> 22.3.1 2023-01-05T00:18:43,760 [notice] To update, run: python3 -m pip install --upgrade pip 2023-01-05T00:18:44,136 Installing build dependencies: finished with status 'done' 2023-01-05T00:18:44,150 Getting requirements to build wheel: started 2023-01-05T00:18:44,151 Running command Getting requirements to build wheel 2023-01-05T00:19:20,757 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-01-05T00:19:20,758 Will attempt to use Cython. 2023-01-05T00:19:20,758 Compiling MDAnalysis/lib/formats/libdcd.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,758 Compiling MDAnalysis/lib/c_distances.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,758 Compiling MDAnalysis/lib/c_distances_openmp.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,758 Compiling MDAnalysis/lib/qcprot.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,758 Compiling MDAnalysis/lib/formats/libmdaxdr.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,759 Compiling MDAnalysis/lib/formats/cython_util.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,759 Compiling MDAnalysis/analysis/encore/cutils.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,759 Compiling MDAnalysis/analysis/encore/clustering/affinityprop.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,759 Compiling MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libc/string.pxd. 2023-01-05T00:19:20,759 Compiling MDAnalysis/lib/_cutil.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-01-05T00:19:20,760 Compiling MDAnalysis/lib/_augment.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-01-05T00:19:20,760 Compiling MDAnalysis/lib/nsgrid.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/vector.pxd. 2023-01-05T00:19:20,760 Compiling MDAnalysis/coordinates/timestep.pyx because it depends on /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/Cython/Includes/libcpp/__init__.pxd. 2023-01-05T00:19:20,760 [ 1/13] Cythonizing MDAnalysis/lib/_augment.pyx 2023-01-05T00:19:20,760 [ 2/13] Cythonizing MDAnalysis/lib/_cutil.pyx 2023-01-05T00:19:20,760 [ 3/13] Cythonizing MDAnalysis/lib/nsgrid.pyx 2023-01-05T00:19:20,761 [ 4/13] Cythonizing MDAnalysis/analysis/encore/clustering/affinityprop.pyx 2023-01-05T00:19:20,761 [ 5/13] Cythonizing MDAnalysis/analysis/encore/cutils.pyx 2023-01-05T00:19:20,761 [ 6/13] Cythonizing MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx 2023-01-05T00:19:20,761 [ 7/13] Cythonizing MDAnalysis/coordinates/timestep.pyx 2023-01-05T00:19:20,761 [ 8/13] Cythonizing MDAnalysis/lib/c_distances.pyx 2023-01-05T00:19:20,761 [ 9/13] Cythonizing MDAnalysis/lib/c_distances_openmp.pyx 2023-01-05T00:19:20,762 [10/13] Cythonizing MDAnalysis/lib/formats/cython_util.pyx 2023-01-05T00:19:20,762 [11/13] Cythonizing MDAnalysis/lib/formats/libdcd.pyx 2023-01-05T00:19:20,762 [12/13] Cythonizing MDAnalysis/lib/formats/libmdaxdr.pyx 2023-01-05T00:19:20,762 [13/13] Cythonizing MDAnalysis/lib/qcprot.pyx 2023-01-05T00:19:21,837 Getting requirements to build wheel: finished with status 'done' 2023-01-05T00:19:21,852 Created temporary directory: /tmp/pip-modern-metadata-0u1da4d0 2023-01-05T00:19:21,855 Preparing metadata (pyproject.toml): started 2023-01-05T00:19:21,856 Running command Preparing metadata (pyproject.toml) 2023-01-05T00:19:24,175 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-01-05T00:19:24,175 Will attempt to use Cython. 2023-01-05T00:19:24,387 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-01-05T00:19:24,387 warnings.warn(msg) 2023-01-05T00:19:24,599 running dist_info 2023-01-05T00:19:24,608 creating /tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info 2023-01-05T00:19:24,615 writing /tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/PKG-INFO 2023-01-05T00:19:24,620 writing dependency_links to /tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/dependency_links.txt 2023-01-05T00:19:24,623 writing requirements to /tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/requires.txt 2023-01-05T00:19:24,624 writing top-level names to /tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/top_level.txt 2023-01-05T00:19:24,626 writing manifest file '/tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/SOURCES.txt' 2023-01-05T00:19:24,673 reading manifest file '/tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/SOURCES.txt' 2023-01-05T00:19:24,676 reading manifest template 'MANIFEST.in' 2023-01-05T00:19:24,849 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-01-05T00:19:24,850 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-01-05T00:19:24,852 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-01-05T00:19:24,853 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-01-05T00:19:24,855 warning: no previously-included files matching '*~' found anywhere in distribution 2023-01-05T00:19:24,856 warning: no previously-included files matching '.git' found anywhere in distribution 2023-01-05T00:19:24,857 adding license file 'LICENSE' 2023-01-05T00:19:24,857 adding license file 'AUTHORS' 2023-01-05T00:19:24,874 writing manifest file '/tmp/pip-modern-metadata-0u1da4d0/MDAnalysis.egg-info/SOURCES.txt' 2023-01-05T00:19:24,877 creating '/tmp/pip-modern-metadata-0u1da4d0/MDAnalysis-2.4.2.dist-info' 2023-01-05T00:19:25,186 Preparing metadata (pyproject.toml): finished with status 'done' 2023-01-05T00:19:25,196 Source in /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980 has version 2.4.2, which satisfies requirement mdanalysis==2.4.2 from https://files.pythonhosted.org/packages/7d/6b/f0ea2ab44ed0a2448737d779e02d3ae719c186dc9e3ce4cd0d75b4026dcc/MDAnalysis-2.4.2.tar.gz 2023-01-05T00:19:25,198 Removed mdanalysis==2.4.2 from https://files.pythonhosted.org/packages/7d/6b/f0ea2ab44ed0a2448737d779e02d3ae719c186dc9e3ce4cd0d75b4026dcc/MDAnalysis-2.4.2.tar.gz from build tracker '/tmp/pip-build-tracker-nk6mpxmq' 2023-01-05T00:19:25,208 Created temporary directory: /tmp/pip-unpack-9i8rm3hr 2023-01-05T00:19:25,208 Building wheels for collected packages: mdanalysis 2023-01-05T00:19:25,213 Created temporary directory: /tmp/pip-wheel-0z1kulei 2023-01-05T00:19:25,214 Destination directory: /tmp/pip-wheel-0z1kulei 2023-01-05T00:19:25,216 Building wheel for mdanalysis (pyproject.toml): started 2023-01-05T00:19:25,217 Running command Building wheel for mdanalysis (pyproject.toml) 2023-01-05T00:19:27,352 Attempting to autodetect OpenMP support... Compiler supports OpenMP 2023-01-05T00:19:27,353 Will attempt to use Cython. 2023-01-05T00:19:27,554 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/config/_apply_pyprojecttoml.py:196: UserWarning: `install_requires` overwritten in `pyproject.toml` (dependencies) 2023-01-05T00:19:27,554 warnings.warn(msg) 2023-01-05T00:19:27,748 running bdist_wheel 2023-01-05T00:19:27,768 running build 2023-01-05T00:19:27,768 running build_py 2023-01-05T00:19:27,774 creating build 2023-01-05T00:19:27,775 creating build/lib.linux-armv7l-cpython-39 2023-01-05T00:19:27,776 creating build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,777 copying MDAnalysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,780 copying MDAnalysis/due.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,782 copying MDAnalysis/exceptions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,784 copying MDAnalysis/units.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,787 copying MDAnalysis/authors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,789 copying MDAnalysis/version.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:27,792 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,793 copying MDAnalysis/transformations/rotate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,795 copying MDAnalysis/transformations/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,798 copying MDAnalysis/transformations/positionaveraging.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,801 copying MDAnalysis/transformations/wrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,803 copying MDAnalysis/transformations/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,806 copying MDAnalysis/transformations/boxdimensions.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,808 copying MDAnalysis/transformations/fit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,810 copying MDAnalysis/transformations/translate.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations 2023-01-05T00:19:27,813 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-01-05T00:19:27,814 copying MDAnalysis/tests/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-01-05T00:19:27,817 copying MDAnalysis/tests/datafiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/tests 2023-01-05T00:19:27,820 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,821 copying MDAnalysis/topology/GMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,824 copying MDAnalysis/topology/TPRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,826 copying MDAnalysis/topology/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,829 copying MDAnalysis/topology/FHIAIMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,831 copying MDAnalysis/topology/PDBQTParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,833 copying MDAnalysis/topology/MMTFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,836 copying MDAnalysis/topology/ExtendedPDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,838 copying MDAnalysis/topology/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,841 copying MDAnalysis/topology/MOL2Parser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,844 copying MDAnalysis/topology/LAMMPSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,847 copying MDAnalysis/topology/XYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,849 copying MDAnalysis/topology/HoomdXMLParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,851 copying MDAnalysis/topology/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,854 copying MDAnalysis/topology/tables.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,856 copying MDAnalysis/topology/GROParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,859 copying MDAnalysis/topology/PQRParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,862 copying MDAnalysis/topology/GSDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,864 copying MDAnalysis/topology/TOPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,867 copying MDAnalysis/topology/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,869 copying MDAnalysis/topology/MinimalParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,872 copying MDAnalysis/topology/ITPParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,875 copying MDAnalysis/topology/DLPolyParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,877 copying MDAnalysis/topology/DMSParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,880 copying MDAnalysis/topology/PSFParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,883 copying MDAnalysis/topology/CRDParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,885 copying MDAnalysis/topology/guessers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,888 copying MDAnalysis/topology/PDBParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,891 copying MDAnalysis/topology/TXYZParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology 2023-01-05T00:19:27,894 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,895 copying MDAnalysis/core/selection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,899 copying MDAnalysis/core/_get_readers.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,902 copying MDAnalysis/core/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,904 copying MDAnalysis/core/topologyattrs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,908 copying MDAnalysis/core/topology.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,911 copying MDAnalysis/core/universe.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,916 copying MDAnalysis/core/accessors.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,918 copying MDAnalysis/core/groups.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,925 copying MDAnalysis/core/topologyobjects.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/core 2023-01-05T00:19:27,929 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,930 copying MDAnalysis/lib/log.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,933 copying MDAnalysis/lib/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,935 copying MDAnalysis/lib/mdamath.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,937 copying MDAnalysis/lib/transformations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,942 copying MDAnalysis/lib/picklable_file_io.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,945 copying MDAnalysis/lib/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,949 copying MDAnalysis/lib/NeighborSearch.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,952 copying MDAnalysis/lib/pkdtree.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,955 copying MDAnalysis/lib/util.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,960 copying MDAnalysis/lib/correlations.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:27,963 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-01-05T00:19:27,964 copying MDAnalysis/visualization/streamlines.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-01-05T00:19:27,967 copying MDAnalysis/visualization/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-01-05T00:19:27,969 copying MDAnalysis/visualization/streamlines_3D.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization 2023-01-05T00:19:27,973 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,974 copying MDAnalysis/converters/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,976 copying MDAnalysis/converters/OpenMMParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,979 copying MDAnalysis/converters/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,982 copying MDAnalysis/converters/RDKitParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,985 copying MDAnalysis/converters/RDKit.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,988 copying MDAnalysis/converters/OpenMM.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,991 copying MDAnalysis/converters/ParmEdParser.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/converters 2023-01-05T00:19:27,994 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:27,995 copying MDAnalysis/selections/pymol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:27,998 copying MDAnalysis/selections/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,000 copying MDAnalysis/selections/gromacs.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,002 copying MDAnalysis/selections/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,005 copying MDAnalysis/selections/vmd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,007 copying MDAnalysis/selections/charmm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,009 copying MDAnalysis/selections/jmol.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/selections 2023-01-05T00:19:28,011 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,012 copying MDAnalysis/auxiliary/XVG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,015 copying MDAnalysis/auxiliary/EDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,018 copying MDAnalysis/auxiliary/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,021 copying MDAnalysis/auxiliary/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,024 copying MDAnalysis/auxiliary/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary 2023-01-05T00:19:28,028 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,029 copying MDAnalysis/analysis/pca.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,032 copying MDAnalysis/analysis/density.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,035 copying MDAnalysis/analysis/rms.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,039 copying MDAnalysis/analysis/contacts.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,041 copying MDAnalysis/analysis/diffusionmap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,044 copying MDAnalysis/analysis/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,047 copying MDAnalysis/analysis/helix_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,050 copying MDAnalysis/analysis/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,052 copying MDAnalysis/analysis/dielectric.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,055 copying MDAnalysis/analysis/rdf.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,058 copying MDAnalysis/analysis/lineardensity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,060 copying MDAnalysis/analysis/polymer.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,063 copying MDAnalysis/analysis/waterdynamics.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,066 copying MDAnalysis/analysis/distances.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,069 copying MDAnalysis/analysis/dihedrals.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,072 copying MDAnalysis/analysis/psa.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,076 copying MDAnalysis/analysis/nucleicacids.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,079 copying MDAnalysis/analysis/leaflet.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,081 copying MDAnalysis/analysis/nuclinfo.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,084 copying MDAnalysis/analysis/align.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,088 copying MDAnalysis/analysis/msd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,091 copying MDAnalysis/analysis/bat.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,094 copying MDAnalysis/analysis/gnm.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:19:28,098 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,100 copying MDAnalysis/coordinates/base.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,103 copying MDAnalysis/coordinates/TRR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,106 copying MDAnalysis/coordinates/MMTF.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,108 copying MDAnalysis/coordinates/memory.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,111 copying MDAnalysis/coordinates/PQR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,114 copying MDAnalysis/coordinates/PDBQT.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,117 copying MDAnalysis/coordinates/GMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,119 copying MDAnalysis/coordinates/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,123 copying MDAnalysis/coordinates/DLPoly.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,126 copying MDAnalysis/coordinates/MOL2.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,128 copying MDAnalysis/coordinates/H5MD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,133 copying MDAnalysis/coordinates/CRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,136 copying MDAnalysis/coordinates/TNG.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,139 copying MDAnalysis/coordinates/TXYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,142 copying MDAnalysis/coordinates/NAMDBIN.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,144 copying MDAnalysis/coordinates/DCD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,148 copying MDAnalysis/coordinates/FHIAIMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,151 copying MDAnalysis/coordinates/XDR.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,154 copying MDAnalysis/coordinates/ParmEd.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,156 copying MDAnalysis/coordinates/core.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,159 copying MDAnalysis/coordinates/DMS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,162 copying MDAnalysis/coordinates/PDB.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,166 copying MDAnalysis/coordinates/chain.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,170 copying MDAnalysis/coordinates/XYZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,173 copying MDAnalysis/coordinates/chemfiles.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,177 copying MDAnalysis/coordinates/TRJ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,181 copying MDAnalysis/coordinates/XTC.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,184 copying MDAnalysis/coordinates/TRZ.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,187 copying MDAnalysis/coordinates/GSD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,190 copying MDAnalysis/coordinates/GRO.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,194 copying MDAnalysis/coordinates/LAMMPS.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,197 copying MDAnalysis/coordinates/INPCRD.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,199 copying MDAnalysis/coordinates/null.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,202 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-01-05T00:19:28,204 copying MDAnalysis/topology/tpr/setting.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-01-05T00:19:28,207 copying MDAnalysis/topology/tpr/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-01-05T00:19:28,209 copying MDAnalysis/topology/tpr/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-01-05T00:19:28,213 copying MDAnalysis/topology/tpr/obj.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr 2023-01-05T00:19:28,216 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,218 copying MDAnalysis/lib/formats/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,221 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-01-05T00:19:28,222 copying MDAnalysis/analysis/hbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-01-05T00:19:28,225 copying MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds 2023-01-05T00:19:28,228 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-01-05T00:19:28,229 copying MDAnalysis/analysis/legacy/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-01-05T00:19:28,232 copying MDAnalysis/analysis/legacy/x3dna.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy 2023-01-05T00:19:28,236 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:19:28,237 copying MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:19:28,241 copying MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:19:28,244 copying MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:19:28,247 copying MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:19:28,252 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-01-05T00:19:28,254 copying MDAnalysis/analysis/hole2/hole.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-01-05T00:19:28,258 copying MDAnalysis/analysis/hole2/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-01-05T00:19:28,261 copying MDAnalysis/analysis/hole2/templates.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-01-05T00:19:28,264 copying MDAnalysis/analysis/hole2/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2 2023-01-05T00:19:28,268 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,269 copying MDAnalysis/analysis/encore/similarity.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,274 copying MDAnalysis/analysis/encore/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,276 copying MDAnalysis/analysis/encore/covariance.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,279 copying MDAnalysis/analysis/encore/confdistmatrix.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,283 copying MDAnalysis/analysis/encore/utils.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,286 copying MDAnalysis/analysis/encore/bootstrap.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:28,289 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-01-05T00:19:28,290 copying MDAnalysis/analysis/data/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-01-05T00:19:28,292 copying MDAnalysis/analysis/data/filenames.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-01-05T00:19:28,296 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:28,297 copying MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:28,300 copying MDAnalysis/analysis/encore/clustering/cluster.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:28,303 copying MDAnalysis/analysis/encore/clustering/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:28,306 copying MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:28,309 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:28,310 copying MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:28,313 copying MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:28,316 copying MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:28,319 running egg_info 2023-01-05T00:19:28,332 writing MDAnalysis.egg-info/PKG-INFO 2023-01-05T00:19:28,336 writing dependency_links to MDAnalysis.egg-info/dependency_links.txt 2023-01-05T00:19:28,338 writing requirements to MDAnalysis.egg-info/requires.txt 2023-01-05T00:19:28,340 writing top-level names to MDAnalysis.egg-info/top_level.txt 2023-01-05T00:19:28,370 reading manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-01-05T00:19:28,383 reading manifest template 'MANIFEST.in' 2023-01-05T00:19:28,577 warning: no previously-included files matching 'doc/html/html' found anywhere in distribution 2023-01-05T00:19:28,580 warning: no previously-included files matching '*.pyc' found anywhere in distribution 2023-01-05T00:19:28,583 warning: no previously-included files matching '*.pyo' found anywhere in distribution 2023-01-05T00:19:28,585 warning: no previously-included files matching '*.pyd' found anywhere in distribution 2023-01-05T00:19:28,588 warning: no previously-included files matching '*~' found anywhere in distribution 2023-01-05T00:19:28,590 warning: no previously-included files matching '.git' found anywhere in distribution 2023-01-05T00:19:28,591 adding license file 'LICENSE' 2023-01-05T00:19:28,591 adding license file 'AUTHORS' 2023-01-05T00:19:28,617 writing manifest file 'MDAnalysis.egg-info/SOURCES.txt' 2023-01-05T00:19:28,621 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.include' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,621 !! 2023-01-05T00:19:28,622 ############################ 2023-01-05T00:19:28,622 # Package would be ignored # 2023-01-05T00:19:28,622 ############################ 2023-01-05T00:19:28,622 Python recognizes 'MDAnalysis.analysis.encore.clustering.include' as an importable package, 2023-01-05T00:19:28,622 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,622 'MDAnalysis.analysis.encore.clustering.include' has been automatically added to the distribution only 2023-01-05T00:19:28,622 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,623 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,623 Please make sure that 'MDAnalysis.analysis.encore.clustering.include' is included as a package by using 2023-01-05T00:19:28,623 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,623 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,623 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,623 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,623 documentation page. 2023-01-05T00:19:28,624 !! 2023-01-05T00:19:28,624 check.warn(importable) 2023-01-05T00:19:28,625 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.clustering.src' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,625 !! 2023-01-05T00:19:28,625 ############################ 2023-01-05T00:19:28,625 # Package would be ignored # 2023-01-05T00:19:28,625 ############################ 2023-01-05T00:19:28,626 Python recognizes 'MDAnalysis.analysis.encore.clustering.src' as an importable package, 2023-01-05T00:19:28,626 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,626 'MDAnalysis.analysis.encore.clustering.src' has been automatically added to the distribution only 2023-01-05T00:19:28,626 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,626 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,626 Please make sure that 'MDAnalysis.analysis.encore.clustering.src' is included as a package by using 2023-01-05T00:19:28,626 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,627 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,627 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,627 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,627 documentation page. 2023-01-05T00:19:28,627 !! 2023-01-05T00:19:28,628 check.warn(importable) 2023-01-05T00:19:28,628 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,628 !! 2023-01-05T00:19:28,628 ############################ 2023-01-05T00:19:28,628 # Package would be ignored # 2023-01-05T00:19:28,628 ############################ 2023-01-05T00:19:28,629 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.include' as an importable package, 2023-01-05T00:19:28,629 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,629 'MDAnalysis.analysis.encore.dimensionality_reduction.include' has been automatically added to the distribution only 2023-01-05T00:19:28,629 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,629 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,629 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.include' is included as a package by using 2023-01-05T00:19:28,630 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,630 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,630 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,630 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,630 documentation page. 2023-01-05T00:19:28,630 !! 2023-01-05T00:19:28,631 check.warn(importable) 2023-01-05T00:19:28,631 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,631 !! 2023-01-05T00:19:28,631 ############################ 2023-01-05T00:19:28,631 # Package would be ignored # 2023-01-05T00:19:28,631 ############################ 2023-01-05T00:19:28,632 Python recognizes 'MDAnalysis.analysis.encore.dimensionality_reduction.src' as an importable package, 2023-01-05T00:19:28,632 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,632 'MDAnalysis.analysis.encore.dimensionality_reduction.src' has been automatically added to the distribution only 2023-01-05T00:19:28,632 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,632 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,632 Please make sure that 'MDAnalysis.analysis.encore.dimensionality_reduction.src' is included as a package by using 2023-01-05T00:19:28,632 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,633 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,633 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,633 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,633 documentation page. 2023-01-05T00:19:28,633 !! 2023-01-05T00:19:28,634 check.warn(importable) 2023-01-05T00:19:28,634 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.include' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,634 !! 2023-01-05T00:19:28,634 ############################ 2023-01-05T00:19:28,634 # Package would be ignored # 2023-01-05T00:19:28,634 ############################ 2023-01-05T00:19:28,634 Python recognizes 'MDAnalysis.lib.formats.include' as an importable package, 2023-01-05T00:19:28,635 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,635 'MDAnalysis.lib.formats.include' has been automatically added to the distribution only 2023-01-05T00:19:28,635 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,635 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,635 Please make sure that 'MDAnalysis.lib.formats.include' is included as a package by using 2023-01-05T00:19:28,635 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,635 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,636 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,636 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,636 documentation page. 2023-01-05T00:19:28,636 !! 2023-01-05T00:19:28,636 check.warn(importable) 2023-01-05T00:19:28,637 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.formats.src' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,637 !! 2023-01-05T00:19:28,637 ############################ 2023-01-05T00:19:28,637 # Package would be ignored # 2023-01-05T00:19:28,637 ############################ 2023-01-05T00:19:28,637 Python recognizes 'MDAnalysis.lib.formats.src' as an importable package, 2023-01-05T00:19:28,637 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,638 'MDAnalysis.lib.formats.src' has been automatically added to the distribution only 2023-01-05T00:19:28,638 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,638 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,638 Please make sure that 'MDAnalysis.lib.formats.src' is included as a package by using 2023-01-05T00:19:28,638 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,638 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,638 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,639 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,639 documentation page. 2023-01-05T00:19:28,639 !! 2023-01-05T00:19:28,639 check.warn(importable) 2023-01-05T00:19:28,639 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.include' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,640 !! 2023-01-05T00:19:28,640 ############################ 2023-01-05T00:19:28,640 # Package would be ignored # 2023-01-05T00:19:28,640 ############################ 2023-01-05T00:19:28,640 Python recognizes 'MDAnalysis.lib.include' as an importable package, 2023-01-05T00:19:28,640 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,641 'MDAnalysis.lib.include' has been automatically added to the distribution only 2023-01-05T00:19:28,641 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,641 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,641 Please make sure that 'MDAnalysis.lib.include' is included as a package by using 2023-01-05T00:19:28,641 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,641 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,641 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,642 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,642 documentation page. 2023-01-05T00:19:28,642 !! 2023-01-05T00:19:28,642 check.warn(importable) 2023-01-05T00:19:28,642 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.libmdanalysis' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,642 !! 2023-01-05T00:19:28,643 ############################ 2023-01-05T00:19:28,643 # Package would be ignored # 2023-01-05T00:19:28,643 ############################ 2023-01-05T00:19:28,643 Python recognizes 'MDAnalysis.lib.libmdanalysis' as an importable package, 2023-01-05T00:19:28,643 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,643 'MDAnalysis.lib.libmdanalysis' has been automatically added to the distribution only 2023-01-05T00:19:28,644 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,644 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,644 Please make sure that 'MDAnalysis.lib.libmdanalysis' is included as a package by using 2023-01-05T00:19:28,644 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,644 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,644 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,645 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,645 documentation page. 2023-01-05T00:19:28,645 !! 2023-01-05T00:19:28,645 check.warn(importable) 2023-01-05T00:19:28,645 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/setuptools/command/build_py.py:202: SetuptoolsDeprecationWarning: Installing 'MDAnalysis.lib.src.transformations' as data is deprecated, please list it in `packages`. 2023-01-05T00:19:28,645 !! 2023-01-05T00:19:28,646 ############################ 2023-01-05T00:19:28,646 # Package would be ignored # 2023-01-05T00:19:28,646 ############################ 2023-01-05T00:19:28,646 Python recognizes 'MDAnalysis.lib.src.transformations' as an importable package, 2023-01-05T00:19:28,646 but it is not listed in the `packages` configuration of setuptools. 2023-01-05T00:19:28,647 'MDAnalysis.lib.src.transformations' has been automatically added to the distribution only 2023-01-05T00:19:28,647 because it may contain data files, but this behavior is likely to change 2023-01-05T00:19:28,647 in future versions of setuptools (and therefore is considered deprecated). 2023-01-05T00:19:28,647 Please make sure that 'MDAnalysis.lib.src.transformations' is included as a package by using 2023-01-05T00:19:28,647 the `packages` configuration field or the proper discovery methods 2023-01-05T00:19:28,647 (for example by using `find_namespace_packages(...)`/`find_namespace:` 2023-01-05T00:19:28,647 instead of `find_packages(...)`/`find:`). 2023-01-05T00:19:28,648 You can read more about "package discovery" and "data files" on setuptools 2023-01-05T00:19:28,648 documentation page. 2023-01-05T00:19:28,648 !! 2023-01-05T00:19:28,648 check.warn(importable) 2023-01-05T00:19:28,650 copying MDAnalysis/analysis/data/rama_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-01-05T00:19:28,655 copying MDAnalysis/analysis/data/janin_ref_data.npy -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data 2023-01-05T00:19:28,659 copying MDAnalysis/lib/_augment.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,692 copying MDAnalysis/lib/_augment.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,695 copying MDAnalysis/lib/_cutil.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,723 copying MDAnalysis/lib/_cutil.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,725 copying MDAnalysis/lib/_cutil.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,728 copying MDAnalysis/lib/c_distances.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,757 copying MDAnalysis/lib/c_distances.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,760 copying MDAnalysis/lib/c_distances_openmp.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,775 copying MDAnalysis/lib/c_distances_openmp.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,778 copying MDAnalysis/lib/nsgrid.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,809 copying MDAnalysis/lib/nsgrid.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,812 copying MDAnalysis/lib/qcprot.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,823 copying MDAnalysis/lib/qcprot.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:28,825 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-01-05T00:19:28,826 copying MDAnalysis/lib/include/calc_distances.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include 2023-01-05T00:19:28,830 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-01-05T00:19:28,831 copying MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis 2023-01-05T00:19:28,833 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-01-05T00:19:28,833 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-01-05T00:19:28,835 copying MDAnalysis/lib/src/transformations/AUTHOR -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-01-05T00:19:28,837 copying MDAnalysis/lib/src/transformations/LICENCE -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-01-05T00:19:28,839 copying MDAnalysis/lib/src/transformations/transformations.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-01-05T00:19:28,844 copying MDAnalysis/coordinates/timestep.cpp -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,864 copying MDAnalysis/coordinates/timestep.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,866 copying MDAnalysis/coordinates/timestep.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:19:28,869 copying MDAnalysis/lib/formats/cython_util.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,890 copying MDAnalysis/lib/formats/cython_util.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,892 copying MDAnalysis/lib/formats/cython_util.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,895 copying MDAnalysis/lib/formats/libdcd.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,923 copying MDAnalysis/lib/formats/libdcd.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,926 copying MDAnalysis/lib/formats/libdcd.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,929 copying MDAnalysis/lib/formats/libmdaxdr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,960 copying MDAnalysis/lib/formats/libmdaxdr.pxd -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,962 copying MDAnalysis/lib/formats/libmdaxdr.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:28,966 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,967 copying MDAnalysis/lib/formats/include/endianswap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,969 copying MDAnalysis/lib/formats/include/fastio.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,972 copying MDAnalysis/lib/formats/include/readdcd.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,976 copying MDAnalysis/lib/formats/include/trr_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,978 copying MDAnalysis/lib/formats/include/xdrfile.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,981 copying MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,983 copying MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,986 copying MDAnalysis/lib/formats/include/xtc_seek.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include 2023-01-05T00:19:28,988 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:28,989 copying MDAnalysis/lib/formats/src/trr_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:28,991 copying MDAnalysis/lib/formats/src/xdrfile.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:28,996 copying MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:28,999 copying MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:29,001 copying MDAnalysis/lib/formats/src/xtc_seek.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:19:29,005 copying MDAnalysis/analysis/encore/cutils.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:29,012 copying MDAnalysis/analysis/encore/cutils.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:19:29,016 copying MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:29,025 copying MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:19:29,028 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-01-05T00:19:29,029 copying MDAnalysis/analysis/encore/clustering/include/ap.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include 2023-01-05T00:19:29,031 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-01-05T00:19:29,032 copying MDAnalysis/analysis/encore/clustering/src/ap.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-01-05T00:19:29,035 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:29,044 copying MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:19:29,046 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-01-05T00:19:29,047 copying MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-01-05T00:19:29,049 creating build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-01-05T00:19:29,050 copying MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-01-05T00:19:29,069 running build_ext 2023-01-05T00:19:29,071 building 'MDAnalysis.lib.formats.libdcd' extension 2023-01-05T00:19:29,071 creating build/temp.linux-armv7l-cpython-39 2023-01-05T00:19:29,072 creating build/temp.linux-armv7l-cpython-39/MDAnalysis 2023-01-05T00:19:29,073 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib 2023-01-05T00:19:29,073 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats 2023-01-05T00:19:29,075 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libdcd.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:19:29,107 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:19:29,459 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:19:29,459 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:19:29,459 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:19:29,459 from MDAnalysis/lib/formats/libdcd.c:781: 2023-01-05T00:19:29,459 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:19:29,459 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:19:29,460 | ^~~~~~~ 2023-01-05T00:19:29,577 In file included from MDAnalysis/lib/formats/libdcd.c:791: 2023-01-05T00:19:29,577 MDAnalysis/lib/formats/include/readdcd.h: In function ‘read_dcdstep’: 2023-01-05T00:19:29,577 MDAnalysis/lib/formats/include/readdcd.h:562:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:19:29,578 562 | if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT; 2023-01-05T00:19:29,578 | ^~ 2023-01-05T00:19:29,581 MDAnalysis/lib/formats/include/readdcd.h: In function ‘write_dcdheader’: 2023-01-05T00:19:29,581 MDAnalysis/lib/formats/include/readdcd.h:698:14: warning: unused variable ‘tmbuf’ [-Wunused-variable] 2023-01-05T00:19:29,582 698 | struct tm *tmbuf; 2023-01-05T00:19:29,582 | ^~~~~ 2023-01-05T00:19:29,582 MDAnalysis/lib/formats/include/readdcd.h:697:10: warning: unused variable ‘cur_time’ [-Wunused-variable] 2023-01-05T00:19:29,582 697 | time_t cur_time; 2023-01-05T00:19:29,583 | ^~~~~~~~ 2023-01-05T00:19:31,306 In file included from MDAnalysis/lib/formats/include/readdcd.h:25, 2023-01-05T00:19:31,306 from MDAnalysis/lib/formats/libdcd.c:791: 2023-01-05T00:19:31,306 At top level: 2023-01-05T00:19:31,307 MDAnalysis/lib/formats/include/endianswap.h:96:13: warning: ‘swap2_aligned’ defined but not used [-Wunused-function] 2023-01-05T00:19:31,307 96 | static void swap2_aligned(void *v, long ndata) { 2023-01-05T00:19:31,307 | ^~~~~~~~~~~~~ 2023-01-05T00:19:31,307 MDAnalysis/lib/formats/include/endianswap.h:32:13: warning: ‘swap2_unaligned’ defined but not used [-Wunused-function] 2023-01-05T00:19:31,307 32 | static void swap2_unaligned(void *v, long ndata) { 2023-01-05T00:19:31,308 | ^~~~~~~~~~~~~~~ 2023-01-05T00:19:31,308 In file included from MDAnalysis/lib/formats/libdcd.c:790: 2023-01-05T00:19:31,308 MDAnalysis/lib/formats/include/fastio.h:453:12: warning: ‘fio_write_str’ defined but not used [-Wunused-function] 2023-01-05T00:19:31,308 453 | static int fio_write_str(fio_fd fd, const char *str) { 2023-01-05T00:19:31,308 | ^~~~~~~~~~~~~ 2023-01-05T00:19:31,308 MDAnalysis/lib/formats/include/fastio.h:449:12: warning: ‘fio_read_int32’ defined but not used [-Wunused-function] 2023-01-05T00:19:31,309 449 | static int fio_read_int32(fio_fd fd, int *i) { 2023-01-05T00:19:31,309 | ^~~~~~~~~~~~~~ 2023-01-05T00:20:02,064 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:20:02,289 building 'MDAnalysis.lib.c_distances' extension 2023-01-05T00:20:02,290 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:20:02,323 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:20:02,668 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:20:02,668 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:20:02,668 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:20:02,668 from MDAnalysis/lib/c_distances.c:781: 2023-01-05T00:20:02,668 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:20:02,669 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:20:02,669 | ^~~~~~~ 2023-01-05T00:20:32,794 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:20:33,027 building 'MDAnalysis.lib.c_distances_openmp' extension 2023-01-05T00:20:33,029 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -DPARALLEL -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/c_distances_openmp.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -fopenmp -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:20:33,057 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:20:33,368 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:20:33,368 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:20:33,368 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:20:33,368 from MDAnalysis/lib/c_distances_openmp.c:792: 2023-01-05T00:20:33,368 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:20:33,368 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:20:33,369 | ^~~~~~~ 2023-01-05T00:20:39,145 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.o -L/usr/lib -lm -lgomp -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -fopenmp 2023-01-05T00:20:39,300 building 'MDAnalysis.lib.qcprot' extension 2023-01-05T00:20:39,301 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/qcprot.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:20:39,329 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:20:39,631 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:20:39,631 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:20:39,632 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:20:39,632 from MDAnalysis/lib/qcprot.c:775: 2023-01-05T00:20:39,632 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:20:39,632 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:20:39,632 | ^~~~~~~ 2023-01-05T00:20:39,690 MDAnalysis/lib/qcprot.c: In function ‘__pyx_pf_10MDAnalysis_3lib_6qcprot_InnerProduct’: 2023-01-05T00:20:39,691 MDAnalysis/lib/qcprot.c:2383:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:20:39,691 2383 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2023-01-05T00:20:39,691 | ^ 2023-01-05T00:20:39,695 MDAnalysis/lib/qcprot.c:2591:35: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:20:39,695 2591 | for (__pyx_t_6 = 0; __pyx_t_6 < __pyx_t_5; __pyx_t_6+=1) { 2023-01-05T00:20:39,695 | ^ 2023-01-05T00:20:45,553 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:20:45,682 building 'MDAnalysis.lib._transformations' extension 2023-01-05T00:20:45,683 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src 2023-01-05T00:20:45,683 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations 2023-01-05T00:20:45,684 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/src/transformations/transformations.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:20:45,712 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:20:46,017 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:20:46,018 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:20:46,018 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:20:46,018 from MDAnalysis/lib/src/transformations/transformations.c:73: 2023-01-05T00:20:46,018 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:20:46,018 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:20:46,018 | ^~~~~~~ 2023-01-05T00:20:46,082 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_superimposition_matrix’: 2023-01-05T00:20:46,082 MDAnalysis/lib/src/transformations/transformations.c:1845: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,082 1845 | #pragma vector always 2023-01-05T00:20:46,082 | 2023-01-05T00:20:46,084 MDAnalysis/lib/src/transformations/transformations.c:1962: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,084 1962 | #pragma vector always 2023-01-05T00:20:46,085 | 2023-01-05T00:20:46,085 MDAnalysis/lib/src/transformations/transformations.c:1986: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,085 1986 | #pragma vector always 2023-01-05T00:20:46,085 | 2023-01-05T00:20:46,089 MDAnalysis/lib/src/transformations/transformations.c: In function ‘axis2tuple’: 2023-01-05T00:20:46,090 MDAnalysis/lib/src/transformations/transformations.c:2122:5: warning: ‘PyUnicode_GetSize’ is deprecated [-Wdeprecated-declarations] 2023-01-05T00:20:46,090 2122 | if (PyUnicode_Check(axes) && (PyUnicode_GetSize(axes) == 4)) { 2023-01-05T00:20:46,090 | ^~ 2023-01-05T00:20:46,090 In file included from /usr/include/python3.9/Python.h:97, 2023-01-05T00:20:46,090 from MDAnalysis/lib/src/transformations/transformations.c:68: 2023-01-05T00:20:46,091 /usr/include/python3.9/unicodeobject.h:177:43: note: declared here 2023-01-05T00:20:46,091 177 | Py_DEPRECATED(3.3) PyAPI_FUNC(Py_ssize_t) PyUnicode_GetSize( 2023-01-05T00:20:46,091 | ^~~~~~~~~~~~~~~~~ 2023-01-05T00:20:46,128 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_vector_norm’: 2023-01-05T00:20:46,128 MDAnalysis/lib/src/transformations/transformations.c:3427: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,128 3427 | #pragma vector always 2023-01-05T00:20:46,129 | 2023-01-05T00:20:46,131 MDAnalysis/lib/src/transformations/transformations.c:3508: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,131 3508 | #pragma vector always 2023-01-05T00:20:46,131 | 2023-01-05T00:20:46,136 MDAnalysis/lib/src/transformations/transformations.c: In function ‘py_unit_vector’: 2023-01-05T00:20:46,137 MDAnalysis/lib/src/transformations/transformations.c:3610: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,137 3610 | #pragma vector always 2023-01-05T00:20:46,137 | 2023-01-05T00:20:46,137 MDAnalysis/lib/src/transformations/transformations.c:3615: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,137 3615 | #pragma vector always 2023-01-05T00:20:46,137 | 2023-01-05T00:20:46,141 MDAnalysis/lib/src/transformations/transformations.c:3679: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,141 3679 | #pragma vector always 2023-01-05T00:20:46,141 | 2023-01-05T00:20:46,141 MDAnalysis/lib/src/transformations/transformations.c:3684: warning: ignoring ‘#pragma vector always’ [-Wunknown-pragmas] 2023-01-05T00:20:46,141 3684 | #pragma vector always 2023-01-05T00:20:46,142 | 2023-01-05T00:20:46,217 At top level: 2023-01-05T00:20:46,217 MDAnalysis/lib/src/transformations/transformations.c:910:1: warning: ‘PyConverter_DoubleVector4Copy’ defined but not used [-Wunused-function] 2023-01-05T00:20:46,217 910 | PyConverter_DoubleVector4Copy( 2023-01-05T00:20:46,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:20:46,218 MDAnalysis/lib/src/transformations/transformations.c:804:1: warning: ‘PyConverter_DoubleArrayOrNone’ defined but not used [-Wunused-function] 2023-01-05T00:20:46,218 804 | PyConverter_DoubleArrayOrNone( 2023-01-05T00:20:46,218 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:20:46,218 MDAnalysis/lib/src/transformations/transformations.c:774:1: warning: ‘PyConverter_DoubleArray’ defined but not used [-Wunused-function] 2023-01-05T00:20:46,218 774 | PyConverter_DoubleArray( 2023-01-05T00:20:46,218 | ^~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:20:52,013 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:20:52,148 building 'MDAnalysis.lib.formats.libmdaxdr' extension 2023-01-05T00:20:52,149 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src 2023-01-05T00:20:52,150 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/libmdaxdr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:20:52,183 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:20:52,490 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:20:52,490 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:20:52,491 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:20:52,491 from MDAnalysis/lib/formats/libmdaxdr.c:802: 2023-01-05T00:20:52,491 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:20:52,491 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:20:52,491 | ^~~~~~~ 2023-01-05T00:20:52,529 In file included from MDAnalysis/lib/formats/libmdaxdr.c:811: 2023-01-05T00:20:52,529 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:20:52,529 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:20:52,529 | 2023-01-05T00:20:52,531 In file included from MDAnalysis/lib/formats/libmdaxdr.c:812: 2023-01-05T00:20:52,531 MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:20:52,532 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:20:52,532 | 2023-01-05T00:20:52,532 In file included from MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-01-05T00:20:52,532 from MDAnalysis/lib/formats/libmdaxdr.c:812: 2023-01-05T00:20:52,533 MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:20:52,533 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:20:52,533 | 2023-01-05T00:20:52,534 In file included from MDAnalysis/lib/formats/libmdaxdr.c:813: 2023-01-05T00:20:52,534 MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:20:52,534 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:20:52,535 | 2023-01-05T00:21:24,445 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/trr_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:24,474 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:24,528 In file included from MDAnalysis/lib/formats/src/trr_seek.c:30: 2023-01-05T00:21:24,528 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:24,528 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:24,528 | 2023-01-05T00:21:24,534 In file included from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-01-05T00:21:24,534 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:24,535 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:24,535 | 2023-01-05T00:21:24,535 In file included from /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-01-05T00:21:24,536 from MDAnalysis/lib/formats/src/trr_seek.c:31: 2023-01-05T00:21:24,536 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:24,536 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:24,536 | 2023-01-05T00:21:24,539 MDAnalysis/lib/formats/src/trr_seek.c: In function ‘read_trr_n_frames’: 2023-01-05T00:21:24,540 MDAnalysis/lib/formats/src/trr_seek.c:39:27: warning: unused variable ‘totalframebytes’ [-Wunused-variable] 2023-01-05T00:21:24,540 39 | int result, framebytes, totalframebytes; 2023-01-05T00:21:24,540 | ^~~~~~~~~~~~~~~ 2023-01-05T00:21:24,540 MDAnalysis/lib/formats/src/trr_seek.c:38:15: warning: unused variable ‘lambda’ [-Wunused-variable] 2023-01-05T00:21:24,540 38 | float time, lambda; 2023-01-05T00:21:24,540 | ^~~~~~ 2023-01-05T00:21:24,541 MDAnalysis/lib/formats/src/trr_seek.c:38:9: warning: unused variable ‘time’ [-Wunused-variable] 2023-01-05T00:21:24,541 38 | float time, lambda; 2023-01-05T00:21:24,541 | ^~~~ 2023-01-05T00:21:24,652 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:24,679 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:24,776 In file included from MDAnalysis/lib/formats/src/xdrfile.c:62: 2023-01-05T00:21:24,777 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:24,777 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:24,777 | 2023-01-05T00:21:24,786 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofint’: 2023-01-05T00:21:24,787 MDAnalysis/lib/formats/src/xdrfile.c:501:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,787 501 | while (size >= num && num_of_bits < 32) 2023-01-05T00:21:24,787 | ^~ 2023-01-05T00:21:24,788 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘sizeofints’: 2023-01-05T00:21:24,788 MDAnalysis/lib/formats/src/xdrfile.c:547:32: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,788 547 | while (bytes[num_of_bytes] >= num) 2023-01-05T00:21:24,788 | ^~ 2023-01-05T00:21:24,790 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘encodeints’: 2023-01-05T00:21:24,790 MDAnalysis/lib/formats/src/xdrfile.c:656:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,790 656 | if (num_of_bits >= num_of_bytes * 8) 2023-01-05T00:21:24,790 | ^~ 2023-01-05T00:21:24,791 MDAnalysis/lib/formats/src/xdrfile.c:658:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,791 658 | for (i = 0; i < num_of_bytes; i++) 2023-01-05T00:21:24,791 | ^ 2023-01-05T00:21:24,792 MDAnalysis/lib/formats/src/xdrfile.c:666:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,792 666 | for (i = 0; i < num_of_bytes-1; i++) 2023-01-05T00:21:24,792 | ^ 2023-01-05T00:21:24,793 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘decodebits’: 2023-01-05T00:21:24,793 MDAnalysis/lib/formats/src/xdrfile.c:706:16: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,793 706 | if (lastbits < num_of_bits) 2023-01-05T00:21:24,793 | ^ 2023-01-05T00:21:24,795 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_decompress_coord_float’: 2023-01-05T00:21:24,796 MDAnalysis/lib/formats/src/xdrfile.c:816:10: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,796 816 | if(size3>xfp->buf1size) 2023-01-05T00:21:24,796 | ^ 2023-01-05T00:21:24,798 MDAnalysis/lib/formats/src/xdrfile.c:868:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,798 868 | maxidx = (LASTIDXxfp->buf1size) 2023-01-05T00:21:24,805 | ^ 2023-01-05T00:21:24,809 MDAnalysis/lib/formats/src/xdrfile.c:1135:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,809 1135 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) 2023-01-05T00:21:24,809 | ^ 2023-01-05T00:21:24,810 MDAnalysis/lib/formats/src/xdrfile.c:1141:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,810 1141 | maxidx = (LASTIDXxfp->buf1size) 2023-01-05T00:21:24,818 | ^ 2023-01-05T00:21:24,820 MDAnalysis/lib/formats/src/xdrfile.c:1368:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,820 1368 | maxidx = (LASTIDXxfp->buf1size) { 2023-01-05T00:21:24,829 | ^ 2023-01-05T00:21:24,835 MDAnalysis/lib/formats/src/xdrfile.c:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare] 2023-01-05T00:21:24,835 1619 | while (smallidx < LASTIDX && magicints[smallidx] < mindiff) { 2023-01-05T00:21:24,835 | ^ 2023-01-05T00:21:24,836 MDAnalysis/lib/formats/src/xdrfile.c:1624:19: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare] 2023-01-05T00:21:24,837 1624 | maxidx = (LASTIDX maxsize) 2023-01-05T00:21:26,496 | ^ 2023-01-05T00:21:26,498 MDAnalysis/lib/formats/src/xdrfile.c:2335:15: note: ‘size’ was declared here 2023-01-05T00:21:26,498 2335 | unsigned int size; 2023-01-05T00:21:26,498 | ^~~~ 2023-01-05T00:21:26,931 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_float’: 2023-01-05T00:21:26,932 MDAnalysis/lib/formats/src/xdrfile.c:1157:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:26,932 1157 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-01-05T00:21:26,932 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:26,933 MDAnalysis/lib/formats/src/xdrfile.c:1156:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:26,933 1156 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-01-05T00:21:26,933 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:26,934 MDAnalysis/lib/formats/src/xdrfile.c:1155:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:26,934 1155 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-01-05T00:21:26,934 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:27,688 MDAnalysis/lib/formats/src/xdrfile.c: In function ‘xdrfile_compress_coord_double’: 2023-01-05T00:21:27,689 MDAnalysis/lib/formats/src/xdrfile.c:1639:21: warning: ‘prevcoord[2]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:27,689 1639 | abs(thiscoord[2] - prevcoord[2]) < larger) { 2023-01-05T00:21:27,689 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:27,690 MDAnalysis/lib/formats/src/xdrfile.c:1638:21: warning: ‘prevcoord[1]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:27,690 1638 | abs(thiscoord[1] - prevcoord[1]) < larger && 2023-01-05T00:21:27,690 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:27,691 MDAnalysis/lib/formats/src/xdrfile.c:1637:21: warning: ‘prevcoord[0]’ may be used uninitialized in this function [-Wmaybe-uninitialized] 2023-01-05T00:21:27,692 1637 | abs(thiscoord[0] - prevcoord[0]) < larger && 2023-01-05T00:21:27,692 | ~~~~~~~~~~~~~^~~~~~~~~~~~~~ 2023-01-05T00:21:28,723 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_trr.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:28,749 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:28,802 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:38: 2023-01-05T00:21:28,802 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:28,802 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:28,802 | 2023-01-05T00:21:28,807 In file included from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-01-05T00:21:28,807 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_trr.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:28,808 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:28,808 | 2023-01-05T00:21:28,808 In file included from /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_trr.h:42, 2023-01-05T00:21:28,809 from MDAnalysis/lib/formats/src/xdrfile_trr.c:39: 2023-01-05T00:21:28,809 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:28,809 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:28,809 | 2023-01-05T00:21:28,811 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘do_trnheader’: 2023-01-05T00:21:28,811 MDAnalysis/lib/formats/src/xdrfile_trr.c:78:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-01-05T00:21:28,812 78 | if (slen != strlen(version) + 1) 2023-01-05T00:21:28,812 | ^~ 2023-01-05T00:21:28,812 MDAnalysis/lib/formats/src/xdrfile_trr.c:86:43: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘unsigned int’} [-Wsign-compare] 2023-01-05T00:21:28,812 86 | if (xdrfile_write_string(version, xd) != (strlen(version) + 1)) 2023-01-05T00:21:28,812 | ^~ 2023-01-05T00:21:28,829 MDAnalysis/lib/formats/src/xdrfile_trr.c: In function ‘write_trr’: 2023-01-05T00:21:28,829 MDAnalysis/lib/formats/src/xdrfile_trr.c:408:10: warning: ‘plcholder’ is used uninitialized in this function [-Wuninitialized] 2023-01-05T00:21:28,829 408 | return do_trn(xd, 0, &step, &t, &lambda, box, &natoms, x, v, f, plcholder); 2023-01-05T00:21:28,829 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:21:29,919 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xdrfile_xtc.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:29,945 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:29,969 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:30: 2023-01-05T00:21:29,969 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:29,969 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:29,970 | 2023-01-05T00:21:29,981 In file included from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-01-05T00:21:29,981 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:29,981 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:29,981 | 2023-01-05T00:21:29,981 In file included from /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-01-05T00:21:29,981 from MDAnalysis/lib/formats/src/xdrfile_xtc.c:31: 2023-01-05T00:21:29,982 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:29,982 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:29,982 | 2023-01-05T00:21:30,107 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64 -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats -I/usr/include/python3.9 -c MDAnalysis/lib/formats/src/xtc_seek.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:30,133 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:30,157 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:25: 2023-01-05T00:21:30,158 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:30,158 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:30,158 | 2023-01-05T00:21:30,170 In file included from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-01-05T00:21:30,171 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_xtc.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:30,171 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:30,171 | 2023-01-05T00:21:30,172 In file included from /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile_xtc.h:43, 2023-01-05T00:21:30,172 from MDAnalysis/lib/formats/src/xtc_seek.c:26: 2023-01-05T00:21:30,172 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/formats/include/xdrfile.h:5:2: warning: "/*" within comment [-Wcomment] 2023-01-05T00:21:30,172 5 | /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- 2023-01-05T00:21:30,172 | 2023-01-05T00:21:30,336 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:21:30,587 building 'MDAnalysis.lib.formats.cython_util' extension 2023-01-05T00:21:30,588 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/formats/cython_util.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -std=c99 -ffast-math -O3 -funroll-loops -fsigned-zeros 2023-01-05T00:21:30,618 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:30,920 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:21:30,920 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:21:30,921 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:21:30,921 from MDAnalysis/lib/formats/cython_util.c:775: 2023-01-05T00:21:30,921 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:21:30,921 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:21:30,921 | ^~~~~~~ 2023-01-05T00:21:47,748 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:21:47,915 building 'MDAnalysis.analysis.encore.cutils' extension 2023-01-05T00:21:47,916 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis 2023-01-05T00:21:47,916 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore 2023-01-05T00:21:47,917 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/cutils.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2023-01-05T00:21:47,946 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:48,252 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:21:48,252 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:21:48,253 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:21:48,253 from MDAnalysis/analysis/encore/cutils.c:775: 2023-01-05T00:21:48,253 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:21:48,253 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:21:48,253 | ^~~~~~~ 2023-01-05T00:21:50,864 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:21:50,983 building 'MDAnalysis.analysis.encore.clustering.affinityprop' extension 2023-01-05T00:21:50,984 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering 2023-01-05T00:21:50,985 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src 2023-01-05T00:21:50,987 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/affinityprop.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2023-01-05T00:21:51,015 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:21:51,330 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:21:51,330 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:21:51,331 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:21:51,331 from MDAnalysis/analysis/encore/clustering/affinityprop.c:781: 2023-01-05T00:21:51,331 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:21:51,331 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:21:51,331 | ^~~~~~~ 2023-01-05T00:22:01,807 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/analysis/encore/clustering/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/clustering/src/ap.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2023-01-05T00:22:01,833 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:22:02,857 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:22:02,999 building 'MDAnalysis.analysis.encore.dimensionality_reduction.stochasticproxembed' extension 2023-01-05T00:22:03,000 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:22:03,000 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-01-05T00:22:03,002 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2023-01-05T00:22:03,029 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:22:03,712 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/analysis/encore/dimensionality_reduction/include -I/usr/include/python3.9 -c MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -std=c99 -ffast-math -funroll-loops -fsigned-zeros -O3 2023-01-05T00:22:03,739 cc1: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:22:04,047 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:22:04,047 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:22:04,047 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:22:04,047 from MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c:781: 2023-01-05T00:22:04,047 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:22:04,048 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:22:04,048 | ^~~~~~~ 2023-01-05T00:22:08,463 arm-linux-gnueabihf-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.o build/temp.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:22:08,596 building 'MDAnalysis.lib._cutil' extension 2023-01-05T00:22:08,597 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/_cutil.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-01-05T00:22:08,629 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:22:08,875 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:22:08,876 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:22:08,876 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:22:08,876 from MDAnalysis/lib/_cutil.cpp:795: 2023-01-05T00:22:08,876 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:22:08,876 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:22:08,876 | ^~~~~~~ 2023-01-05T00:22:11,759 In file included from MDAnalysis/lib/_cutil.cpp:824: 2023-01-05T00:22:11,759 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,759 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,759 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,760 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,760 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,760 | ^~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,760 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,760 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,761 | ^~~~~~~~~~~~~~ 2023-01-05T00:22:11,761 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,761 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,761 | ^~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,761 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,761 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,762 | ^~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,762 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,762 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,762 | ^~~~~~~~~~~ 2023-01-05T00:22:11,762 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,763 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,763 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,763 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,763 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,763 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,763 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,763 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-01-05T00:22:11,764 | ^~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,764 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,764 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-01-05T00:22:11,764 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,764 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,764 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-01-05T00:22:11,764 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,764 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,765 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-01-05T00:22:11,765 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,765 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,765 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-01-05T00:22:11,765 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,765 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,765 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-01-05T00:22:11,766 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,766 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,766 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-01-05T00:22:11,766 | ^~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:22:11,766 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:116:13: warning: ‘void _ortho_pbc(float (*)[3], uint64_t, float*)’ defined but not used [-Wunused-function] 2023-01-05T00:22:11,766 116 | static void _ortho_pbc(coordinate* coords, uint64_t numcoords, float* box) 2023-01-05T00:22:11,766 | ^~~~~~~~~~ 2023-01-05T00:22:38,164 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.o -L/usr/lib -lm -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:22:38,536 building 'MDAnalysis.lib._augment' extension 2023-01-05T00:22:38,537 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/lib/_augment.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-01-05T00:22:38,570 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:22:38,801 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:22:38,801 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:22:38,801 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:22:38,801 from MDAnalysis/lib/_augment.cpp:790: 2023-01-05T00:22:38,801 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:22:38,801 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:22:38,801 | ^~~~~~~ 2023-01-05T00:23:04,404 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:23:04,748 building 'MDAnalysis.lib.nsgrid' extension 2023-01-05T00:23:04,749 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include -I/usr/include/python3.9 -c MDAnalysis/lib/nsgrid.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-01-05T00:23:04,782 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:23:07,205 In file included from MDAnalysis/lib/nsgrid.cpp:791: 2023-01-05T00:23:07,205 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:827:13: warning: ‘void _calc_dihedral_triclinic(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,205 827 | static void _calc_dihedral_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,205 | ^~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,205 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:791:13: warning: ‘void _calc_dihedral_ortho(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,206 791 | static void _calc_dihedral_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,206 | ^~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,206 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:764:13: warning: ‘void _calc_dihedral(float (*)[3], float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,206 764 | static void _calc_dihedral(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,206 | ^~~~~~~~~~~~~~ 2023-01-05T00:23:07,206 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:689:13: warning: ‘void _calc_angle_triclinic(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,207 689 | static void _calc_angle_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,207 | ^~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,207 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:647:13: warning: ‘void _calc_angle_ortho(float (*)[3], float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,207 647 | static void _calc_angle_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,207 | ^~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,207 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:618:13: warning: ‘void _calc_angle(float (*)[3], float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,208 618 | static void _calc_angle(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,208 | ^~~~~~~~~~~ 2023-01-05T00:23:07,208 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:596:13: warning: ‘void _calc_bond_distance_triclinic(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,208 596 | static void _calc_bond_distance_triclinic(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,208 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,208 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:573:13: warning: ‘void _calc_bond_distance_ortho(float (*)[3], float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,208 573 | static void _calc_bond_distance_ortho(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,208 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,209 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:557:13: warning: ‘void _calc_bond_distance(float (*)[3], float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,209 557 | static void _calc_bond_distance(coordinate* atom1, coordinate* atom2, 2023-01-05T00:23:07,209 | ^~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,209 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:505:13: warning: ‘void _calc_self_distance_array_triclinic(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,209 505 | static void _calc_self_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-01-05T00:23:07,209 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,209 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:472:13: warning: ‘void _calc_self_distance_array_ortho(float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,210 472 | static void _calc_self_distance_array_ortho(coordinate* ref, uint64_t numref, 2023-01-05T00:23:07,210 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,210 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:448:13: warning: ‘void _calc_self_distance_array(float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,210 448 | static void _calc_self_distance_array(coordinate* ref, uint64_t numref, 2023-01-05T00:23:07,210 | ^~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,210 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:424:13: warning: ‘void _calc_distance_array_triclinic(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,210 424 | static void _calc_distance_array_triclinic(coordinate* ref, uint64_t numref, 2023-01-05T00:23:07,211 | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,211 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:399:13: warning: ‘void _calc_distance_array_ortho(float (*)[3], uint64_t, float (*)[3], uint64_t, float*, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,211 399 | static void _calc_distance_array_ortho(coordinate* ref, uint64_t numref, coordinate* conf, 2023-01-05T00:23:07,211 | ^~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:07,211 /tmp/pip-wheel-38g4xyr9/mdanalysis_cdc570327ecd4bdc9415797e67c11980/MDAnalysis/lib/include/calc_distances.h:381:13: warning: ‘void _calc_distance_array(float (*)[3], uint64_t, float (*)[3], uint64_t, double*)’ defined but not used [-Wunused-function] 2023-01-05T00:23:07,211 381 | static void _calc_distance_array(coordinate* ref, uint64_t numref, coordinate* conf, 2023-01-05T00:23:07,211 | ^~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:29,796 In file included from /usr/include/c++/10/vector:72, 2023-01-05T00:23:29,797 from MDAnalysis/lib/nsgrid.cpp:789: 2023-01-05T00:23:29,797 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator]’: 2023-01-05T00:23:29,797 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-01-05T00:23:29,797 426 | vector<_Tp, _Alloc>:: 2023-01-05T00:23:29,797 | ^~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:29,833 In file included from /usr/include/c++/10/vector:67, 2023-01-05T00:23:29,834 from MDAnalysis/lib/nsgrid.cpp:789: 2023-01-05T00:23:29,834 /usr/include/c++/10/bits/stl_vector.h: In function ‘void __pyx_f_10MDAnalysis_3lib_6nsgrid_9NSResults_add_neighbors(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, int, int, double)’: 2023-01-05T00:23:29,834 /usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-01-05T00:23:29,834 1198 | _M_realloc_insert(end(), __x); 2023-01-05T00:23:29,834 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~ 2023-01-05T00:23:29,871 In file included from /usr/include/c++/10/vector:72, 2023-01-05T00:23:29,871 from MDAnalysis/lib/nsgrid.cpp:789: 2023-01-05T00:23:29,871 /usr/include/c++/10/bits/vector.tcc: In member function ‘void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator]’: 2023-01-05T00:23:29,871 /usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type ‘std::vector::iterator’ changed in GCC 7.1 2023-01-05T00:23:29,872 426 | vector<_Tp, _Alloc>:: 2023-01-05T00:23:29,872 | ^~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:30,123 /usr/include/c++/10/bits/vector.tcc: In function ‘PyObject* __pyx_f_10MDAnalysis_3lib_6nsgrid___pyx_unpickle_NSResults__set_state(__pyx_obj_10MDAnalysis_3lib_6nsgrid_NSResults*, PyObject*)’: 2023-01-05T00:23:30,123 /usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type ‘__gnu_cxx::__normal_iterator >’ changed in GCC 7.1 2023-01-05T00:23:30,123 121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...); 2023-01-05T00:23:30,123 | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2023-01-05T00:23:33,471 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:23:33,838 building 'MDAnalysis.coordinates.timestep' extension 2023-01-05T00:23:33,839 creating build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates 2023-01-05T00:23:33,840 arm-linux-gnueabihf-gcc -pthread -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -ffile-prefix-map=/python3.9-3.9.2=. -fstack-protector-strong -Wformat -Werror=format-security -g -fwrapv -O2 -fPIC -I/tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include -I/usr/include/python3.9 -c MDAnalysis/coordinates/timestep.cpp -o build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -ffast-math -O3 -funroll-loops -fsigned-zeros -std=c++11 2023-01-05T00:23:33,872 cc1plus: warning: ‘-fassociative-math’ disabled; other options take precedence 2023-01-05T00:23:34,107 In file included from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarraytypes.h:1944, 2023-01-05T00:23:34,107 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/ndarrayobject.h:12, 2023-01-05T00:23:34,107 from /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/arrayobject.h:4, 2023-01-05T00:23:34,107 from MDAnalysis/coordinates/timestep.cpp:791: 2023-01-05T00:23:34,108 /tmp/pip-build-env-4g47ji3o/overlay/lib/python3.9/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] 2023-01-05T00:23:34,108 17 | #warning "Using deprecated NumPy API, disable it with " \ 2023-01-05T00:23:34,108 | ^~~~~~~ 2023-01-05T00:23:52,205 arm-linux-gnueabihf-g++ -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fwrapv -O2 build/temp.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.o -L/usr/lib -o build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so 2023-01-05T00:23:52,434 installing to build/bdist.linux-armv7l/wheel 2023-01-05T00:23:52,434 running install 2023-01-05T00:23:52,460 running install_lib 2023-01-05T00:23:52,466 creating build/bdist.linux-armv7l 2023-01-05T00:23:52,466 creating build/bdist.linux-armv7l/wheel 2023-01-05T00:23:52,468 creating build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:52,469 creating build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,470 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/rotate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,473 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,476 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/positionaveraging.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,479 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/wrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,481 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,483 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/boxdimensions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,486 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/fit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,488 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/transformations/translate.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/transformations 2023-01-05T00:23:52,491 creating build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-01-05T00:23:52,492 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-01-05T00:23:52,494 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/tests/datafiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/tests 2023-01-05T00:23:52,497 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,498 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,500 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TPRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,502 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,505 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/FHIAIMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,507 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBQTParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,510 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MMTFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,512 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ExtendedPDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,514 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,517 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MOL2Parser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,520 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/LAMMPSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,523 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/XYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,525 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/HoomdXMLParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,527 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,529 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tables.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,532 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GROParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,534 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PQRParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,537 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/GSDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,539 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TOPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,542 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,544 creating build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-01-05T00:23:52,545 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/setting.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-01-05T00:23:52,548 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-01-05T00:23:52,550 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-01-05T00:23:52,553 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/tpr/obj.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology/tpr 2023-01-05T00:23:52,555 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/MinimalParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,557 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/ITPParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,560 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DLPolyParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,562 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/DMSParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,565 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PSFParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,567 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/CRDParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,570 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/guessers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,572 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/PDBParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,575 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/topology/TXYZParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/topology 2023-01-05T00:23:52,578 creating build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,579 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/selection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,583 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/_get_readers.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,585 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,587 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyattrs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,592 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topology.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,595 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/universe.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,599 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/accessors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,602 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/groups.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,608 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/core/topologyobjects.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/core 2023-01-05T00:23:52,613 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,614 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,617 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,620 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,648 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,689 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,734 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,783 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/log.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,786 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,788 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-01-05T00:23:52,789 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/libmdanalysis/__init__.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/libmdanalysis 2023-01-05T00:23:52,791 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,799 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,809 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/mdamath.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,812 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,846 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,887 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-01-05T00:23:52,888 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/include/calc_distances.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/include 2023-01-05T00:23:52,892 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,895 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/transformations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:52,901 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,902 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,905 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,907 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,911 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,913 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/fastio.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,916 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_trr.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,918 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile_xtc.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,921 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xdrfile.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,924 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/readdcd.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,927 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/xtc_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,930 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/endianswap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,932 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/include/trr_seek.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/include 2023-01-05T00:23:52,934 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,975 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:52,995 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,028 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,075 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,078 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,079 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/trr_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,082 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xtc_seek.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,085 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_xtc.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,087 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,091 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/src/xdrfile_trr.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats/src 2023-01-05T00:23:53,094 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,098 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libmdaxdr.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,100 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,103 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,139 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/formats 2023-01-05T00:23:53,238 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,266 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/picklable_file_io.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,269 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,274 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,284 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_augment.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,287 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,295 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances_openmp.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,298 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/NeighborSearch.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,301 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src 2023-01-05T00:23:53,303 creating build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-01-05T00:23:53,304 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/AUTHOR -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-01-05T00:23:53,307 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/LICENCE -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-01-05T00:23:53,309 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/src/transformations/transformations.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib/src/transformations 2023-01-05T00:23:53,314 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/c_distances.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,318 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/pkdtree.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,320 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/qcprot.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,332 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/util.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,336 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,338 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/_cutil.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,369 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/lib/correlations.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/lib 2023-01-05T00:23:53,372 creating build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-01-05T00:23:53,374 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-01-05T00:23:53,377 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-01-05T00:23:53,380 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/visualization/streamlines_3D.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/visualization 2023-01-05T00:23:53,383 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,386 creating build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,387 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,390 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMMParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,393 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,396 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKitParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,399 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/RDKit.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,403 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/OpenMM.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,405 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/converters/ParmEdParser.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/converters 2023-01-05T00:23:53,408 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/due.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,411 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/exceptions.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,413 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/units.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,416 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/authors.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,419 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/version.py -> build/bdist.linux-armv7l/wheel/MDAnalysis 2023-01-05T00:23:53,421 creating build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,423 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/pymol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,425 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,428 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/gromacs.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,431 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,433 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/vmd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,436 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/charmm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,438 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/selections/jmol.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/selections 2023-01-05T00:23:53,441 creating build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,442 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/XVG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,445 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/EDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,448 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,452 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,456 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/auxiliary/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/auxiliary 2023-01-05T00:23:53,458 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,460 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/pca.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,464 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/density.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,467 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rms.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,471 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/contacts.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,474 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/diffusionmap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,477 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,481 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-01-05T00:23:53,482 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-01-05T00:23:53,485 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hbonds 2023-01-05T00:23:53,487 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/helix_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,491 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,493 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dielectric.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,496 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/rdf.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,499 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/lineardensity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,502 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/polymer.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,505 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/waterdynamics.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,508 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/distances.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,512 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-01-05T00:23:53,513 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-01-05T00:23:53,516 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/legacy/x3dna.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/legacy 2023-01-05T00:23:53,520 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/dihedrals.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,525 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:23:53,527 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:23:53,532 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:23:53,535 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:23:53,539 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hydrogenbonds 2023-01-05T00:23:53,546 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-01-05T00:23:53,548 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/hole.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-01-05T00:23:53,553 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-01-05T00:23:53,557 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/templates.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-01-05T00:23:53,560 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/hole2/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/hole2 2023-01-05T00:23:53,563 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/psa.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,570 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,571 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/similarity.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,577 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,578 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusteringMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,582 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/cluster.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,585 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,588 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-01-05T00:23:53,589 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/include/ap.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/include 2023-01-05T00:23:53,592 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,606 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,609 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/affinityprop.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,621 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-01-05T00:23:53,623 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/src/ap.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering/src 2023-01-05T00:23:53,627 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/clustering/ClusterCollection.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/clustering 2023-01-05T00:23:53,630 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,640 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,648 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,651 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/covariance.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,655 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,656 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,668 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,671 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-01-05T00:23:53,672 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/include 2023-01-05T00:23:53,675 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,679 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-01-05T00:23:53,680 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction/src 2023-01-05T00:23:53,683 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,687 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,689 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore/dimensionality_reduction 2023-01-05T00:23:53,700 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/confdistmatrix.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,703 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/cutils.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,706 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/utils.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,709 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/encore/bootstrap.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/encore 2023-01-05T00:23:53,712 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nucleicacids.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,716 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/leaflet.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,718 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/nuclinfo.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,721 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/align.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,725 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/msd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,728 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/bat.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,731 creating build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-01-05T00:23:53,732 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/rama_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-01-05T00:23:53,736 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-01-05T00:23:53,738 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/filenames.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-01-05T00:23:53,740 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/data/janin_ref_data.npy -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis/data 2023-01-05T00:23:53,744 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/analysis/gnm.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/analysis 2023-01-05T00:23:53,747 creating build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,748 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/base.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,752 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,754 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MMTF.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,756 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/memory.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,759 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PQR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,762 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDBQT.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,764 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,767 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/__init__.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,770 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DLPoly.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,773 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/MOL2.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,775 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/H5MD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,779 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/CRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,781 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TNG.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,784 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pxd -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,786 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TXYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,788 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/NAMDBIN.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,791 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DCD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,793 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/FHIAIMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,796 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XDR.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,798 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/ParmEd.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,800 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/core.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,802 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/DMS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,804 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/PDB.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,808 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chain.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,811 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XYZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,813 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/chemfiles.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,816 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRJ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,819 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/XTC.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,822 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/TRZ.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,824 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GSD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,827 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/GRO.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,829 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/LAMMPS.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,832 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.pyx -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,835 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,865 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/INPCRD.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,867 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/null.py -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,869 copying build/lib.linux-armv7l-cpython-39/MDAnalysis/coordinates/timestep.cpp -> build/bdist.linux-armv7l/wheel/MDAnalysis/coordinates 2023-01-05T00:23:53,888 running install_egg_info 2023-01-05T00:23:53,894 Copying MDAnalysis.egg-info to build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.2-py3.9.egg-info 2023-01-05T00:23:53,909 running install_scripts 2023-01-05T00:23:54,003 creating build/bdist.linux-armv7l/wheel/MDAnalysis-2.4.2.dist-info/WHEEL 2023-01-05T00:23:54,006 creating '/tmp/pip-wheel-0z1kulei/.tmp-wo4ctdze/MDAnalysis-2.4.2-cp39-cp39-linux_armv7l.whl' and adding 'build/bdist.linux-armv7l/wheel' to it 2023-01-05T00:23:54,009 adding 'MDAnalysis/__init__.py' 2023-01-05T00:23:54,011 adding 'MDAnalysis/authors.py' 2023-01-05T00:23:54,012 adding 'MDAnalysis/due.py' 2023-01-05T00:23:54,014 adding 'MDAnalysis/exceptions.py' 2023-01-05T00:23:54,016 adding 'MDAnalysis/units.py' 2023-01-05T00:23:54,018 adding 'MDAnalysis/version.py' 2023-01-05T00:23:54,020 adding 'MDAnalysis/analysis/__init__.py' 2023-01-05T00:23:54,028 adding 'MDAnalysis/analysis/align.py' 2023-01-05T00:23:54,031 adding 'MDAnalysis/analysis/base.py' 2023-01-05T00:23:54,035 adding 'MDAnalysis/analysis/bat.py' 2023-01-05T00:23:54,038 adding 'MDAnalysis/analysis/contacts.py' 2023-01-05T00:23:54,043 adding 'MDAnalysis/analysis/density.py' 2023-01-05T00:23:54,045 adding 'MDAnalysis/analysis/dielectric.py' 2023-01-05T00:23:54,047 adding 'MDAnalysis/analysis/diffusionmap.py' 2023-01-05T00:23:54,051 adding 'MDAnalysis/analysis/dihedrals.py' 2023-01-05T00:23:54,053 adding 'MDAnalysis/analysis/distances.py' 2023-01-05T00:23:54,055 adding 'MDAnalysis/analysis/gnm.py' 2023-01-05T00:23:54,058 adding 'MDAnalysis/analysis/helix_analysis.py' 2023-01-05T00:23:54,060 adding 'MDAnalysis/analysis/leaflet.py' 2023-01-05T00:23:54,063 adding 'MDAnalysis/analysis/lineardensity.py' 2023-01-05T00:23:54,065 adding 'MDAnalysis/analysis/msd.py' 2023-01-05T00:23:54,067 adding 'MDAnalysis/analysis/nucleicacids.py' 2023-01-05T00:23:54,070 adding 'MDAnalysis/analysis/nuclinfo.py' 2023-01-05T00:23:54,074 adding 'MDAnalysis/analysis/pca.py' 2023-01-05T00:23:54,077 adding 'MDAnalysis/analysis/polymer.py' 2023-01-05T00:23:54,087 adding 'MDAnalysis/analysis/psa.py' 2023-01-05T00:23:54,090 adding 'MDAnalysis/analysis/rdf.py' 2023-01-05T00:23:54,095 adding 'MDAnalysis/analysis/rms.py' 2023-01-05T00:23:54,100 adding 'MDAnalysis/analysis/waterdynamics.py' 2023-01-05T00:23:54,102 adding 'MDAnalysis/analysis/data/__init__.py' 2023-01-05T00:23:54,103 adding 'MDAnalysis/analysis/data/filenames.py' 2023-01-05T00:23:54,107 adding 'MDAnalysis/analysis/data/janin_ref_data.npy' 2023-01-05T00:23:54,112 adding 'MDAnalysis/analysis/data/rama_ref_data.npy' 2023-01-05T00:23:54,115 adding 'MDAnalysis/analysis/encore/__init__.py' 2023-01-05T00:23:54,117 adding 'MDAnalysis/analysis/encore/bootstrap.py' 2023-01-05T00:23:54,119 adding 'MDAnalysis/analysis/encore/confdistmatrix.py' 2023-01-05T00:23:54,121 adding 'MDAnalysis/analysis/encore/covariance.py' 2023-01-05T00:23:54,142 adding 'MDAnalysis/analysis/encore/cutils.c' 2023-01-05T00:23:54,179 adding 'MDAnalysis/analysis/encore/cutils.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:54,182 adding 'MDAnalysis/analysis/encore/cutils.pyx' 2023-01-05T00:23:54,188 adding 'MDAnalysis/analysis/encore/similarity.py' 2023-01-05T00:23:54,191 adding 'MDAnalysis/analysis/encore/utils.py' 2023-01-05T00:23:54,193 adding 'MDAnalysis/analysis/encore/clustering/ClusterCollection.py' 2023-01-05T00:23:54,196 adding 'MDAnalysis/analysis/encore/clustering/ClusteringMethod.py' 2023-01-05T00:23:54,197 adding 'MDAnalysis/analysis/encore/clustering/__init__.py' 2023-01-05T00:23:54,228 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.c' 2023-01-05T00:23:54,334 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:54,339 adding 'MDAnalysis/analysis/encore/clustering/affinityprop.pyx' 2023-01-05T00:23:54,341 adding 'MDAnalysis/analysis/encore/clustering/cluster.py' 2023-01-05T00:23:54,343 adding 'MDAnalysis/analysis/encore/clustering/include/ap.h' 2023-01-05T00:23:54,346 adding 'MDAnalysis/analysis/encore/clustering/src/ap.c' 2023-01-05T00:23:54,348 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/DimensionalityReductionMethod.py' 2023-01-05T00:23:54,350 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/__init__.py' 2023-01-05T00:23:54,352 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/reduce_dimensionality.py' 2023-01-05T00:23:54,375 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.c' 2023-01-05T00:23:54,443 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:54,446 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/stochasticproxembed.pyx' 2023-01-05T00:23:54,448 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/include/spe.h' 2023-01-05T00:23:54,451 adding 'MDAnalysis/analysis/encore/dimensionality_reduction/src/spe.c' 2023-01-05T00:23:54,453 adding 'MDAnalysis/analysis/hbonds/__init__.py' 2023-01-05T00:23:54,454 adding 'MDAnalysis/analysis/hbonds/hbond_autocorrel.py' 2023-01-05T00:23:54,457 adding 'MDAnalysis/analysis/hole2/__init__.py' 2023-01-05T00:23:54,463 adding 'MDAnalysis/analysis/hole2/hole.py' 2023-01-05T00:23:54,465 adding 'MDAnalysis/analysis/hole2/templates.py' 2023-01-05T00:23:54,468 adding 'MDAnalysis/analysis/hole2/utils.py' 2023-01-05T00:23:54,470 adding 'MDAnalysis/analysis/hydrogenbonds/__init__.py' 2023-01-05T00:23:54,475 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py' 2023-01-05T00:23:54,478 adding 'MDAnalysis/analysis/hydrogenbonds/hbond_autocorrel.py' 2023-01-05T00:23:54,488 adding 'MDAnalysis/analysis/hydrogenbonds/wbridge_analysis.py' 2023-01-05T00:23:54,490 adding 'MDAnalysis/analysis/legacy/__init__.py' 2023-01-05T00:23:54,494 adding 'MDAnalysis/analysis/legacy/x3dna.py' 2023-01-05T00:23:54,498 adding 'MDAnalysis/auxiliary/EDR.py' 2023-01-05T00:23:54,500 adding 'MDAnalysis/auxiliary/XVG.py' 2023-01-05T00:23:54,503 adding 'MDAnalysis/auxiliary/__init__.py' 2023-01-05T00:23:54,509 adding 'MDAnalysis/auxiliary/base.py' 2023-01-05T00:23:54,511 adding 'MDAnalysis/auxiliary/core.py' 2023-01-05T00:23:54,513 adding 'MDAnalysis/converters/OpenMM.py' 2023-01-05T00:23:54,515 adding 'MDAnalysis/converters/OpenMMParser.py' 2023-01-05T00:23:54,517 adding 'MDAnalysis/converters/ParmEd.py' 2023-01-05T00:23:54,519 adding 'MDAnalysis/converters/ParmEdParser.py' 2023-01-05T00:23:54,525 adding 'MDAnalysis/converters/RDKit.py' 2023-01-05T00:23:54,527 adding 'MDAnalysis/converters/RDKitParser.py' 2023-01-05T00:23:54,529 adding 'MDAnalysis/converters/__init__.py' 2023-01-05T00:23:54,532 adding 'MDAnalysis/coordinates/CRD.py' 2023-01-05T00:23:54,535 adding 'MDAnalysis/coordinates/DCD.py' 2023-01-05T00:23:54,537 adding 'MDAnalysis/coordinates/DLPoly.py' 2023-01-05T00:23:54,538 adding 'MDAnalysis/coordinates/DMS.py' 2023-01-05T00:23:54,540 adding 'MDAnalysis/coordinates/FHIAIMS.py' 2023-01-05T00:23:54,542 adding 'MDAnalysis/coordinates/GMS.py' 2023-01-05T00:23:54,545 adding 'MDAnalysis/coordinates/GRO.py' 2023-01-05T00:23:54,547 adding 'MDAnalysis/coordinates/GSD.py' 2023-01-05T00:23:54,555 adding 'MDAnalysis/coordinates/H5MD.py' 2023-01-05T00:23:54,557 adding 'MDAnalysis/coordinates/INPCRD.py' 2023-01-05T00:23:54,560 adding 'MDAnalysis/coordinates/LAMMPS.py' 2023-01-05T00:23:54,562 adding 'MDAnalysis/coordinates/MMTF.py' 2023-01-05T00:23:54,565 adding 'MDAnalysis/coordinates/MOL2.py' 2023-01-05T00:23:54,566 adding 'MDAnalysis/coordinates/NAMDBIN.py' 2023-01-05T00:23:54,573 adding 'MDAnalysis/coordinates/PDB.py' 2023-01-05T00:23:54,576 adding 'MDAnalysis/coordinates/PDBQT.py' 2023-01-05T00:23:54,579 adding 'MDAnalysis/coordinates/PQR.py' 2023-01-05T00:23:54,580 adding 'MDAnalysis/coordinates/ParmEd.py' 2023-01-05T00:23:54,583 adding 'MDAnalysis/coordinates/TNG.py' 2023-01-05T00:23:54,589 adding 'MDAnalysis/coordinates/TRJ.py' 2023-01-05T00:23:54,591 adding 'MDAnalysis/coordinates/TRR.py' 2023-01-05T00:23:54,594 adding 'MDAnalysis/coordinates/TRZ.py' 2023-01-05T00:23:54,596 adding 'MDAnalysis/coordinates/TXYZ.py' 2023-01-05T00:23:54,598 adding 'MDAnalysis/coordinates/XDR.py' 2023-01-05T00:23:54,600 adding 'MDAnalysis/coordinates/XTC.py' 2023-01-05T00:23:54,603 adding 'MDAnalysis/coordinates/XYZ.py' 2023-01-05T00:23:54,608 adding 'MDAnalysis/coordinates/__init__.py' 2023-01-05T00:23:54,616 adding 'MDAnalysis/coordinates/base.py' 2023-01-05T00:23:54,620 adding 'MDAnalysis/coordinates/chain.py' 2023-01-05T00:23:54,623 adding 'MDAnalysis/coordinates/chemfiles.py' 2023-01-05T00:23:54,624 adding 'MDAnalysis/coordinates/core.py' 2023-01-05T00:23:54,628 adding 'MDAnalysis/coordinates/memory.py' 2023-01-05T00:23:54,629 adding 'MDAnalysis/coordinates/null.py' 2023-01-05T00:23:54,689 adding 'MDAnalysis/coordinates/timestep.cpp' 2023-01-05T00:23:54,920 adding 'MDAnalysis/coordinates/timestep.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:54,928 adding 'MDAnalysis/coordinates/timestep.pxd' 2023-01-05T00:23:54,932 adding 'MDAnalysis/coordinates/timestep.pyx' 2023-01-05T00:23:54,935 adding 'MDAnalysis/core/__init__.py' 2023-01-05T00:23:54,937 adding 'MDAnalysis/core/_get_readers.py' 2023-01-05T00:23:54,939 adding 'MDAnalysis/core/accessors.py' 2023-01-05T00:23:54,959 adding 'MDAnalysis/core/groups.py' 2023-01-05T00:23:54,967 adding 'MDAnalysis/core/selection.py' 2023-01-05T00:23:54,970 adding 'MDAnalysis/core/topology.py' 2023-01-05T00:23:54,980 adding 'MDAnalysis/core/topologyattrs.py' 2023-01-05T00:23:54,985 adding 'MDAnalysis/core/topologyobjects.py' 2023-01-05T00:23:54,993 adding 'MDAnalysis/core/universe.py' 2023-01-05T00:23:54,996 adding 'MDAnalysis/lib/NeighborSearch.py' 2023-01-05T00:23:54,998 adding 'MDAnalysis/lib/__init__.py' 2023-01-05T00:23:55,073 adding 'MDAnalysis/lib/_augment.cpp' 2023-01-05T00:23:55,347 adding 'MDAnalysis/lib/_augment.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:55,357 adding 'MDAnalysis/lib/_augment.pyx' 2023-01-05T00:23:55,439 adding 'MDAnalysis/lib/_cutil.cpp' 2023-01-05T00:23:55,789 adding 'MDAnalysis/lib/_cutil.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:55,801 adding 'MDAnalysis/lib/_cutil.pxd' 2023-01-05T00:23:55,804 adding 'MDAnalysis/lib/_cutil.pyx' 2023-01-05T00:23:55,860 adding 'MDAnalysis/lib/_transformations.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:55,955 adding 'MDAnalysis/lib/c_distances.c' 2023-01-05T00:23:56,284 adding 'MDAnalysis/lib/c_distances.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:56,297 adding 'MDAnalysis/lib/c_distances.pyx' 2023-01-05T00:23:56,321 adding 'MDAnalysis/lib/c_distances_openmp.c' 2023-01-05T00:23:56,383 adding 'MDAnalysis/lib/c_distances_openmp.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:56,386 adding 'MDAnalysis/lib/c_distances_openmp.pyx' 2023-01-05T00:23:56,389 adding 'MDAnalysis/lib/correlations.py' 2023-01-05T00:23:56,395 adding 'MDAnalysis/lib/distances.py' 2023-01-05T00:23:56,397 adding 'MDAnalysis/lib/log.py' 2023-01-05T00:23:56,400 adding 'MDAnalysis/lib/mdamath.py' 2023-01-05T00:23:56,485 adding 'MDAnalysis/lib/nsgrid.cpp' 2023-01-05T00:23:56,818 adding 'MDAnalysis/lib/nsgrid.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:56,832 adding 'MDAnalysis/lib/nsgrid.pyx' 2023-01-05T00:23:56,834 adding 'MDAnalysis/lib/picklable_file_io.py' 2023-01-05T00:23:56,836 adding 'MDAnalysis/lib/pkdtree.py' 2023-01-05T00:23:56,868 adding 'MDAnalysis/lib/qcprot.c' 2023-01-05T00:23:56,945 adding 'MDAnalysis/lib/qcprot.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:56,949 adding 'MDAnalysis/lib/qcprot.pyx' 2023-01-05T00:23:56,957 adding 'MDAnalysis/lib/transformations.py' 2023-01-05T00:23:56,969 adding 'MDAnalysis/lib/util.py' 2023-01-05T00:23:56,971 adding 'MDAnalysis/lib/formats/__init__.py' 2023-01-05T00:23:57,038 adding 'MDAnalysis/lib/formats/cython_util.c' 2023-01-05T00:23:57,249 adding 'MDAnalysis/lib/formats/cython_util.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:57,256 adding 'MDAnalysis/lib/formats/cython_util.pxd' 2023-01-05T00:23:57,259 adding 'MDAnalysis/lib/formats/cython_util.pyx' 2023-01-05T00:23:57,357 adding 'MDAnalysis/lib/formats/libdcd.c' 2023-01-05T00:23:57,741 adding 'MDAnalysis/lib/formats/libdcd.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:57,754 adding 'MDAnalysis/lib/formats/libdcd.pxd' 2023-01-05T00:23:57,758 adding 'MDAnalysis/lib/formats/libdcd.pyx' 2023-01-05T00:23:57,855 adding 'MDAnalysis/lib/formats/libmdaxdr.c' 2023-01-05T00:23:58,275 adding 'MDAnalysis/lib/formats/libmdaxdr.cpython-39-arm-linux-gnueabihf.so' 2023-01-05T00:23:58,289 adding 'MDAnalysis/lib/formats/libmdaxdr.pxd' 2023-01-05T00:23:58,293 adding 'MDAnalysis/lib/formats/libmdaxdr.pyx' 2023-01-05T00:23:58,295 adding 'MDAnalysis/lib/formats/include/endianswap.h' 2023-01-05T00:23:58,297 adding 'MDAnalysis/lib/formats/include/fastio.h' 2023-01-05T00:23:58,301 adding 'MDAnalysis/lib/formats/include/readdcd.h' 2023-01-05T00:23:58,302 adding 'MDAnalysis/lib/formats/include/trr_seek.h' 2023-01-05T00:23:58,305 adding 'MDAnalysis/lib/formats/include/xdrfile.h' 2023-01-05T00:23:58,307 adding 'MDAnalysis/lib/formats/include/xdrfile_trr.h' 2023-01-05T00:23:58,308 adding 'MDAnalysis/lib/formats/include/xdrfile_xtc.h' 2023-01-05T00:23:58,309 adding 'MDAnalysis/lib/formats/include/xtc_seek.h' 2023-01-05T00:23:58,312 adding 'MDAnalysis/lib/formats/src/trr_seek.c' 2023-01-05T00:23:58,318 adding 'MDAnalysis/lib/formats/src/xdrfile.c' 2023-01-05T00:23:58,321 adding 'MDAnalysis/lib/formats/src/xdrfile_trr.c' 2023-01-05T00:23:58,322 adding 'MDAnalysis/lib/formats/src/xdrfile_xtc.c' 2023-01-05T00:23:58,324 adding 'MDAnalysis/lib/formats/src/xtc_seek.c' 2023-01-05T00:23:58,327 adding 'MDAnalysis/lib/include/calc_distances.h' 2023-01-05T00:23:58,329 adding 'MDAnalysis/lib/libmdanalysis/__init__.pxd' 2023-01-05T00:23:58,332 adding 'MDAnalysis/lib/src/transformations/AUTHOR' 2023-01-05T00:23:58,333 adding 'MDAnalysis/lib/src/transformations/LICENCE' 2023-01-05T00:23:58,343 adding 'MDAnalysis/lib/src/transformations/transformations.c' 2023-01-05T00:23:58,346 adding 'MDAnalysis/selections/__init__.py' 2023-01-05T00:23:58,348 adding 'MDAnalysis/selections/base.py' 2023-01-05T00:23:58,350 adding 'MDAnalysis/selections/charmm.py' 2023-01-05T00:23:58,351 adding 'MDAnalysis/selections/gromacs.py' 2023-01-05T00:23:58,352 adding 'MDAnalysis/selections/jmol.py' 2023-01-05T00:23:58,354 adding 'MDAnalysis/selections/pymol.py' 2023-01-05T00:23:58,355 adding 'MDAnalysis/selections/vmd.py' 2023-01-05T00:23:58,358 adding 'MDAnalysis/tests/__init__.py' 2023-01-05T00:23:58,359 adding 'MDAnalysis/tests/datafiles.py' 2023-01-05T00:23:58,362 adding 'MDAnalysis/topology/CRDParser.py' 2023-01-05T00:23:58,363 adding 'MDAnalysis/topology/DLPolyParser.py' 2023-01-05T00:23:58,365 adding 'MDAnalysis/topology/DMSParser.py' 2023-01-05T00:23:58,367 adding 'MDAnalysis/topology/ExtendedPDBParser.py' 2023-01-05T00:23:58,368 adding 'MDAnalysis/topology/FHIAIMSParser.py' 2023-01-05T00:23:58,370 adding 'MDAnalysis/topology/GMSParser.py' 2023-01-05T00:23:58,372 adding 'MDAnalysis/topology/GROParser.py' 2023-01-05T00:23:58,373 adding 'MDAnalysis/topology/GSDParser.py' 2023-01-05T00:23:58,375 adding 'MDAnalysis/topology/HoomdXMLParser.py' 2023-01-05T00:23:58,378 adding 'MDAnalysis/topology/ITPParser.py' 2023-01-05T00:23:58,381 adding 'MDAnalysis/topology/LAMMPSParser.py' 2023-01-05T00:23:58,383 adding 'MDAnalysis/topology/MMTFParser.py' 2023-01-05T00:23:58,385 adding 'MDAnalysis/topology/MOL2Parser.py' 2023-01-05T00:23:58,387 adding 'MDAnalysis/topology/MinimalParser.py' 2023-01-05T00:23:58,389 adding 'MDAnalysis/topology/PDBParser.py' 2023-01-05T00:23:58,391 adding 'MDAnalysis/topology/PDBQTParser.py' 2023-01-05T00:23:58,393 adding 'MDAnalysis/topology/PQRParser.py' 2023-01-05T00:23:58,395 adding 'MDAnalysis/topology/PSFParser.py' 2023-01-05T00:23:58,397 adding 'MDAnalysis/topology/ParmEdParser.py' 2023-01-05T00:23:58,399 adding 'MDAnalysis/topology/TOPParser.py' 2023-01-05T00:23:58,402 adding 'MDAnalysis/topology/TPRParser.py' 2023-01-05T00:23:58,403 adding 'MDAnalysis/topology/TXYZParser.py' 2023-01-05T00:23:58,405 adding 'MDAnalysis/topology/XYZParser.py' 2023-01-05T00:23:58,407 adding 'MDAnalysis/topology/__init__.py' 2023-01-05T00:23:58,409 adding 'MDAnalysis/topology/base.py' 2023-01-05T00:23:58,410 adding 'MDAnalysis/topology/core.py' 2023-01-05T00:23:58,413 adding 'MDAnalysis/topology/guessers.py' 2023-01-05T00:23:58,415 adding 'MDAnalysis/topology/tables.py' 2023-01-05T00:23:58,418 adding 'MDAnalysis/topology/tpr/__init__.py' 2023-01-05T00:23:58,419 adding 'MDAnalysis/topology/tpr/obj.py' 2023-01-05T00:23:58,421 adding 'MDAnalysis/topology/tpr/setting.py' 2023-01-05T00:23:58,425 adding 'MDAnalysis/topology/tpr/utils.py' 2023-01-05T00:23:58,428 adding 'MDAnalysis/transformations/__init__.py' 2023-01-05T00:23:58,430 adding 'MDAnalysis/transformations/base.py' 2023-01-05T00:23:58,431 adding 'MDAnalysis/transformations/boxdimensions.py' 2023-01-05T00:23:58,433 adding 'MDAnalysis/transformations/fit.py' 2023-01-05T00:23:58,435 adding 'MDAnalysis/transformations/positionaveraging.py' 2023-01-05T00:23:58,437 adding 'MDAnalysis/transformations/rotate.py' 2023-01-05T00:23:58,438 adding 'MDAnalysis/transformations/translate.py' 2023-01-05T00:23:58,440 adding 'MDAnalysis/transformations/wrap.py' 2023-01-05T00:23:58,442 adding 'MDAnalysis/visualization/__init__.py' 2023-01-05T00:23:58,445 adding 'MDAnalysis/visualization/streamlines.py' 2023-01-05T00:23:58,448 adding 'MDAnalysis/visualization/streamlines_3D.py' 2023-01-05T00:23:58,452 adding 'MDAnalysis-2.4.2.dist-info/AUTHORS' 2023-01-05T00:23:58,456 adding 'MDAnalysis-2.4.2.dist-info/LICENSE' 2023-01-05T00:23:58,460 adding 'MDAnalysis-2.4.2.dist-info/METADATA' 2023-01-05T00:23:58,462 adding 'MDAnalysis-2.4.2.dist-info/WHEEL' 2023-01-05T00:23:58,463 adding 'MDAnalysis-2.4.2.dist-info/top_level.txt' 2023-01-05T00:23:58,467 adding 'MDAnalysis-2.4.2.dist-info/RECORD' 2023-01-05T00:23:58,564 removing build/bdist.linux-armv7l/wheel 2023-01-05T00:23:58,891 Building wheel for mdanalysis (pyproject.toml): finished with status 'done' 2023-01-05T00:23:59,080 Created wheel for mdanalysis: filename=MDAnalysis-2.4.2-cp39-cp39-linux_armv7l.whl size=7775772 sha256=05d70a930acb47af383673c351e087e42ab57747d7e0f7f9d72f448abf991dce 2023-01-05T00:23:59,082 Stored in directory: /tmp/pip-ephem-wheel-cache-xcakz8j_/wheels/4a/1a/03/d0f86eb591fb41dfcd8647fff33cdb81b737e76df310945f92 2023-01-05T00:23:59,111 Successfully built mdanalysis 2023-01-05T00:23:59,373 Removed build tracker: '/tmp/pip-build-tracker-nk6mpxmq'